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Ryan CW, Regan SL, Mills EF, McGrath BT, Gong E, Lai YT, Sheingold JB, Patel K, Horowitz T, Moccia A, Tsan YC, Srivastava A, Bielas SL. RING1 missense variants reveal sensitivity of DNA damage repair to H2A monoubiquitination dosage during neurogenesis. Nat Commun 2024; 15:7931. [PMID: 39256363 DOI: 10.1038/s41467-024-52292-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2023] [Accepted: 08/30/2024] [Indexed: 09/12/2024] Open
Abstract
Polycomb repressive complex 1 (PRC1) modifies chromatin through catalysis of histone H2A lysine 119 monoubiquitination (H2AK119ub1). RING1 and RNF2 interchangeably serve as the catalytic subunit within PRC1. Pathogenic missense variants in PRC1 core components reveal functions of these proteins that are obscured in knockout models. While Ring1a knockout models remain healthy, the microcephaly and neuropsychiatric phenotypes associated with a pathogenic RING1 missense variant implicate unappreciated functions. Using an in vitro model of neurodevelopment, we observe that RING1 contributes to the broad placement of H2AK119ub1, and that its targets overlap with those of RNF2. PRC1 complexes harboring hypomorphic RING1 bind target loci but do not catalyze H2AK119ub1, reducing H2AK119ub1 by preventing catalytically active complexes from accessing the locus. This results in delayed DNA damage repair and cell cycle progression in neural progenitor cells (NPCs). Conversely, reduced H2AK119ub1 due to hypomorphic RING1 does not generate differential expression that impacts NPC differentiation. In contrast, hypomorphic RNF2 generates a greater reduction in H2AK119ub1 that results in both delayed DNA repair and widespread transcriptional changes. These findings suggest that the DNA damage response is more sensitive to H2AK119ub1 dosage change than is regulation of gene expression.
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Affiliation(s)
- C W Ryan
- Cellular and Molecular Biology Program, University of Michigan Medical School, Ann Arbor, MI, USA
- Medical Science Training Program, University of Michigan Medical School, Ann Arbor, MI, USA
- Department of Human Genetics, University of Michigan Medical School, Ann Arbor, MI, USA
| | - S L Regan
- Department of Human Genetics, University of Michigan Medical School, Ann Arbor, MI, USA
| | - E F Mills
- Department of Human Genetics, University of Michigan Medical School, Ann Arbor, MI, USA
| | - B T McGrath
- Department of Human Genetics, University of Michigan Medical School, Ann Arbor, MI, USA
| | - E Gong
- Department of Human Genetics, University of Michigan Medical School, Ann Arbor, MI, USA
| | - Y T Lai
- Department of Human Genetics, University of Michigan Medical School, Ann Arbor, MI, USA
| | - J B Sheingold
- Department of Human Genetics, University of Michigan Medical School, Ann Arbor, MI, USA
| | - K Patel
- Department of Human Genetics, University of Michigan Medical School, Ann Arbor, MI, USA
| | - T Horowitz
- Department of Human Genetics, University of Michigan Medical School, Ann Arbor, MI, USA
| | - A Moccia
- Department of Human Genetics, University of Michigan Medical School, Ann Arbor, MI, USA
| | - Y C Tsan
- Department of Human Genetics, University of Michigan Medical School, Ann Arbor, MI, USA
| | - A Srivastava
- Department of Human Genetics, University of Michigan Medical School, Ann Arbor, MI, USA
- Sanjay Gandhi Postgraduate Institute of Medical Sciences, Department of Medical Genetics, Lucknow, India
| | - S L Bielas
- Cellular and Molecular Biology Program, University of Michigan Medical School, Ann Arbor, MI, USA.
- Department of Human Genetics, University of Michigan Medical School, Ann Arbor, MI, USA.
- Department of Pediatrics, University of Michigan Medical School, Ann Arbor, MI, USA.
- Neuroscience Graduate Program, University of Michigan Medical School, Ann Arbor, MI, USA.
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2
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Jeliazkova N, Longhin E, El Yamani N, Rundén-Pran E, Moschini E, Serchi T, Vrček IV, Burgum MJ, Doak SH, Cimpan MR, Rios-Mondragon I, Cimpan E, Battistelli CL, Bossa C, Tsekovska R, Drobne D, Novak S, Repar N, Ammar A, Nymark P, Di Battista V, Sosnowska A, Puzyn T, Kochev N, Iliev L, Jeliazkov V, Reilly K, Lynch I, Bakker M, Delpivo C, Sánchez Jiménez A, Fonseca AS, Manier N, Fernandez-Cruz ML, Rashid S, Willighagen E, D Apostolova M, Dusinska M. A template wizard for the cocreation of machine-readable data-reporting to harmonize the evaluation of (nano)materials. Nat Protoc 2024; 19:2642-2684. [PMID: 38755447 DOI: 10.1038/s41596-024-00993-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2023] [Accepted: 02/20/2024] [Indexed: 05/18/2024]
Abstract
Making research data findable, accessible, interoperable and reusable (FAIR) is typically hampered by a lack of skills in technical aspects of data management by data generators and a lack of resources. We developed a Template Wizard for researchers to easily create templates suitable for consistently capturing data and metadata from their experiments. The templates are easy to use and enable the compilation of machine-readable metadata to accompany data generation and align them to existing community standards and databases, such as eNanoMapper, streamlining the adoption of the FAIR principles. These templates are citable objects and are available as online tools. The Template Wizard is designed to be user friendly and facilitates using and reusing existing templates for new projects or project extensions. The wizard is accompanied by an online template validator, which allows self-evaluation of the template (to ensure mapping to the data schema and machine readability of the captured data) and transformation by an open-source parser into machine-readable formats, compliant with the FAIR principles. The templates are based on extensive collective experience in nanosafety data collection and include over 60 harmonized data entry templates for physicochemical characterization and hazard assessment (cell viability, genotoxicity, environmental organism dose-response tests, omics), as well as exposure and release studies. The templates are generalizable across fields and have already been extended and adapted for microplastics and advanced materials research. The harmonized templates improve the reliability of interlaboratory comparisons, data reuse and meta-analyses and can facilitate the safety evaluation and regulation process for (nano) materials.
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Affiliation(s)
| | - Eleonora Longhin
- Health Effects Laboratory, Department of Environmental Chemistry & Health Effects, The Climate and Environmental Research Institute NILU, Kjeller, Norway
| | - Naouale El Yamani
- Health Effects Laboratory, Department of Environmental Chemistry & Health Effects, The Climate and Environmental Research Institute NILU, Kjeller, Norway
| | - Elise Rundén-Pran
- Health Effects Laboratory, Department of Environmental Chemistry & Health Effects, The Climate and Environmental Research Institute NILU, Kjeller, Norway
| | - Elisa Moschini
- Environmental Health group, Department of Environmental Research and Innovation, Luxembourg Institute of Science and Technology, Belvaux, Luxembourg
| | - Tommaso Serchi
- Environmental Health group, Department of Environmental Research and Innovation, Luxembourg Institute of Science and Technology, Belvaux, Luxembourg
| | | | - Michael J Burgum
- In Vitro Toxicology Group, Faculty of Medicine, Health and Life Sciences, Institute of Life Sciences, Swansea University Medical School, Singleton Park, Swansea, Wales, UK
| | - Shareen H Doak
- In Vitro Toxicology Group, Faculty of Medicine, Health and Life Sciences, Institute of Life Sciences, Swansea University Medical School, Singleton Park, Swansea, Wales, UK
| | | | | | - Emil Cimpan
- Department of Computer Science, Electrical Engineering and Mathematical Sciences, Western Norway University of Applied Sciences, Bergen, Norway
| | | | - Cecilia Bossa
- Environment and Health Department, Istituto Superiore di Sanità, Rome, Italy
| | - Rositsa Tsekovska
- Medical and Biological Research Laboratory, Roumen Tsanev Institute of Molecular Biology-Bulgarian Academy of Sciences, Sofia, Bulgaria
| | - Damjana Drobne
- Department of Biology, Biotechnical Faculty, University of Ljubljana, Ljubljana, Slovenia
| | - Sara Novak
- Department of Biology, Biotechnical Faculty, University of Ljubljana, Ljubljana, Slovenia
| | - Neža Repar
- Department of Biology, Biotechnical Faculty, University of Ljubljana, Ljubljana, Slovenia
| | - Ammar Ammar
- Department of Bioinformatics-BiGCaT, NUTRIM, Maastricht University, Maastricht, the Netherlands
| | - Penny Nymark
- Institute of Environmental Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Veronica Di Battista
- BASF SE, Material Physics, Carl Bosch straße, Ludwigshafen, Germany
- Department of Environmental and Resource Engineering, DTU, Kgs. Lyngby, Denmark
| | - Anita Sosnowska
- QSAR Lab Ltd., Gdańsk, Poland
- University of Gdańsk, Faculty of Chemistry, Gdansk, Poland
| | - Tomasz Puzyn
- QSAR Lab Ltd., Gdańsk, Poland
- University of Gdańsk, Faculty of Chemistry, Gdansk, Poland
| | - Nikolay Kochev
- Ideaconsult Ltd., Sofia, Bulgaria
- Department of Analytical Chemistry and Computer Chemistry, Faculty of Chemistry, University of Plovdiv, Plovdiv, Bulgaria
| | | | | | - Katie Reilly
- School of Geography, Earth and Environmental Sciences, University of Birmingham, Birmingham, UK
| | - Iseult Lynch
- School of Geography, Earth and Environmental Sciences, University of Birmingham, Birmingham, UK
| | - Martine Bakker
- National Institute for Public Health and the Environment, Bilthoven, the Netherlands
| | | | - Araceli Sánchez Jiménez
- Spanish National Institute of Health and Safety, Centro Nacional de Verificación de Maquinaria, Barakaldo, Spain
| | - Ana Sofia Fonseca
- National Research Centre for the Working Environment, Copenhagen, Denmark
| | - Nicolas Manier
- Ecotoxicology of Substances and Environmental Matrices Unit, French National Institute for Industrial Environment and Risks, Verneuil-en-Halatte, France
| | - María Luisa Fernandez-Cruz
- Department of Environment and Agronomy, National Institute for Agriculture and Food Research and Technology, Spanish National Research Council, Madrid, Spain
| | - Shahzad Rashid
- Institute of Occupational Medicine, Research Avenue North, Edinburgh, UK
| | - Egon Willighagen
- Department of Bioinformatics-BiGCaT, NUTRIM, Maastricht University, Maastricht, the Netherlands
| | - Margarita D Apostolova
- Medical and Biological Research Laboratory, Roumen Tsanev Institute of Molecular Biology-Bulgarian Academy of Sciences, Sofia, Bulgaria
| | - Maria Dusinska
- Health Effects Laboratory, Department of Environmental Chemistry & Health Effects, The Climate and Environmental Research Institute NILU, Kjeller, Norway.
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Nordengen AL, Zheng C, Krutto A, Kværner AS, Alavi DT, Henriksen HB, Henriksen C, Smeland S, Bøhn SK, Paur I, Shaposhnikov S, Collins AR, Blomhoff R. Effect of a personalized intensive dietary intervention on base excision repair (BER) in colorectal cancer patients: Results from a randomized controlled trial. Free Radic Biol Med 2024; 218:178-189. [PMID: 38588903 DOI: 10.1016/j.freeradbiomed.2024.04.211] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/23/2024] [Revised: 03/23/2024] [Accepted: 04/03/2024] [Indexed: 04/10/2024]
Abstract
DNA repair is essential to maintain genomic integrity and may affect colorectal cancer (CRC) patients' risk of secondary cancers, treatment efficiency, and susceptibility to various comorbidities. Bioactive compounds identified in plant foods have the potential to modulate DNA repair mechanisms, but there is limited evidence of how dietary factors may affect DNA repair activity in CRC patients in remission after surgery. The aim of this study was to investigate the effect of a 6-month personalized intensive dietary intervention on DNA repair activity in post-surgery CRC patients (stage I-III). The present study included patients from the randomized controlled trial CRC-NORDIET, enrolled 2-9 months after surgery. The intervention group received an intensive dietary intervention emphasizing a prudent diet with specific plant-based foods suggested to dampen inflammation and oxidative stress, while the control group received only standard care advice. The comet-based in vitro repair assay was applied to assess DNA repair activity, specifically base excision repair (BER), in peripheral blood mononuclear cells (PBMCs). Statistical analyses were conducted using gamma generalized linear mixed models (Gamma GLMM). A total of 138 CRC patients were included, 72 from the intervention group and 66 from the control group. The BER activity in the intervention group did not change significantly compared to the control group. Our findings revealed a substantial range in both inter- and intra-individual levels of BER. In conclusion, the results do not support an effect of dietary intervention on BER activity in post-surgery CRC patients during a 6-month intervention period.
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Affiliation(s)
- Anne Lene Nordengen
- Department of Nutrition, Institute of Basic Medical Sciences, University of Oslo, Norway; Norgenotech AS, Oslo Cancer Cluster Incubator, Oslo, Norway; Department of Sport Science and Physical Education, Faculty of Health and Sport Sciences, University of Agder, Kristiansand, Norway.
| | - Congying Zheng
- Norgenotech AS, Oslo Cancer Cluster Incubator, Oslo, Norway; Department of Pharmacology and Toxicology, NUTRIM School of Nutrition and Translation Research in Metabolism, Maastricht University, Maastricht, Netherlands
| | - Annika Krutto
- Department of Biostatistics, Institute of Basic Medical Sciences, University of Oslo, Norway
| | - Ane S Kværner
- Section for Colorectal Cancer Screening, Cancer Registry of Norway, Norwegian Institute of Public Health, Oslo, Norway
| | - Dena T Alavi
- Department of Nutrition, Institute of Basic Medical Sciences, University of Oslo, Norway
| | - Hege B Henriksen
- Department of Nutrition, Institute of Basic Medical Sciences, University of Oslo, Norway
| | - Christine Henriksen
- Department of Nutrition, Institute of Basic Medical Sciences, University of Oslo, Norway
| | - Sigbjørn Smeland
- Division of Cancer Medicine, Oslo University Hospital, Oslo, Norway; Institute of Clinical Medicine, University of Norway, Oslo, Norway
| | - Siv K Bøhn
- Faculty of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences, Ås, Norway
| | - Ingvild Paur
- Department of Nutrition, Institute of Basic Medical Sciences, University of Oslo, Norway; Norwegian Advisory Unit on Disease-Related Undernutrition, Oslo University Hospital, Oslo, Norway; Department of Clinical Service, Division of Cancer Medicine, Oslo University Hospital, Oslo, Norway
| | | | | | - Rune Blomhoff
- Department of Nutrition, Institute of Basic Medical Sciences, University of Oslo, Norway; Department of Clinical Service, Division of Cancer Medicine, Oslo University Hospital, Oslo, Norway
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Collia M, Møller P, Langie SAS, Vettorazzi A, Azqueta A. Further development of CometChip technology to measure DNA damage in vitro and in vivo: Comparison with the 2 gels/slide format of the standard and enzyme-modified comet assay. Toxicology 2024; 501:153690. [PMID: 38040084 DOI: 10.1016/j.tox.2023.153690] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2023] [Revised: 11/17/2023] [Accepted: 11/27/2023] [Indexed: 12/03/2023]
Abstract
DNA damage plays a pivotal role in carcinogenesis and other diseases. The comet assay has been used for more than three decades to measure DNA damages. The 1-2 gels/slide format is the most used version of the assay. In 2010, a high throughput 96 macrowell format with a spatially encoded array of microwells patterned in agarose was developed, called the CometChip. The commercial version (CometChip®) has been used for the in vitro standard version of the comet assay (following the manufacturer's protocol), although it has not been compared directly with the 2 gels/slide format. The aim of this work is to developed new protocols to allow use of DNA repair enzymes as well as the analysis of in vivo frozen tissue samples in the CometChip®, to increase the throughput, and to compare its performance with the classic 2 gels/slide format. We adapted the manufacturer's protocol to allow the use of snap frozen tissue samples, using male Wistar rats orally dosed with methyl methanesulfonate (MMS, 200 mg/kg b.w.), and to detect altered nucleobases using DNA repair enzymes, with TK6 cells treated with potassium bromate (KBrO3, 0-4 mM, 3 h) and formamidopyrimidine DNA glycosylase (Fpg) as the enzyme. Regarding the standard version of the comet, we performed thee comparison of the 2 gel/slide and CometChip® format (using the the manufacturer's protocol), using TK6 cells with MMS (100-800 µM, 1 h) and hydrogen peroxide (H2O2, 7.7-122.5 µM, 5 min) as testing compounds. In all cases the CometChip® was performed along with the 2 gels/slide format. Results obtained were comparable and the CometChip® is a good alternative to the 2 gels/slide format when a higher throughput is required.
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Affiliation(s)
- Miguel Collia
- Department of Pharmaceutical Sciences, School of Pharmacy and Nutrition, University of Navarra, Pamplona, Spain
| | - Peter Møller
- Department of Public Health, Section of Environmental Health, University of Copenhagen, Copenhagen, Denmark
| | - Sabine A S Langie
- Department of Pharmacology & Toxicology, School for Nutrition and Translational Research in Metabolism (NUTRIM), Maastricht University, Maastricht, the Netherlands
| | - Ariane Vettorazzi
- Department of Pharmaceutical Sciences, School of Pharmacy and Nutrition, University of Navarra, Pamplona, Spain
| | - Amaya Azqueta
- Department of Pharmaceutical Sciences, School of Pharmacy and Nutrition, University of Navarra, Pamplona, Spain.
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5
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Mircheva A, Vangrieken P, Al-Nasiry S, van Schooten FJ, Godschalk RWL, Langie SAS. Optimizing the Comet Assay-Based In Vitro DNA Repair Assay for Placental Tissue: A Pilot Study with Pre-Eclamptic Patients. Int J Mol Sci 2023; 25:187. [PMID: 38203356 PMCID: PMC10779140 DOI: 10.3390/ijms25010187] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2023] [Revised: 12/15/2023] [Accepted: 12/19/2023] [Indexed: 01/12/2024] Open
Abstract
The comet assay-based in vitro DNA repair assay has become a common tool for quantifying base excision repair (BER) activity in human lymphocytes or cultured cells. Here, we optimized the protocol for studying BER in human placental tissue because the placenta is a non-invasive tissue for biomonitoring of early-life exposures, and it can be used to investigate molecular mechanisms associated with prenatal disorders. The optimal protein concentration of placental protein extracts for optimal damage recognition and incision was 2 mg protein/mL. The addition of aphidicolin did not lead to reduced non-specific incisions and was, therefore, not included in the optimized protocol. The interval between sample collection and analysis did not affect BER activity up to 70 min. Finally, this optimized protocol was tested on pre-eclamptic (PE) placental tissues (n = 11) and significantly lower BER activity in PE placentas compared to controls (n = 9) was observed. This was paralleled by a significant reduction in the expression of BER-related genes and increased DNA oxidation in PE placentas. Our study indicates that BER activity can be determined in placentas, and lower activity is present in PE compared with healthy. These findings should be followed up in prospective clinical investigations to examine BER's role in the advancement of PE.
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Affiliation(s)
- Anastasiya Mircheva
- Department of Pharmacology and Toxicology, School for Nutrition and Translational Research in Metabolism (NUTRIM), Maastricht University, P.O. Box 616, 6200 MD Maastricht, The Netherlands; (A.M.); (R.W.L.G.)
| | - Philippe Vangrieken
- Department of Internal Medicine, School of Cardiovascular diseases (CARIM), Maastricht University, P.O. Box 616, 6200 MD Maastricht, The Netherlands
| | - Salwan Al-Nasiry
- Department of Obstetrics and Gynecology, Maastricht University Medical Center+, P. Debyelaan 25, 6229 HX Maastricht, The Netherlands
| | - Frederik-Jan van Schooten
- Department of Pharmacology and Toxicology, School for Nutrition and Translational Research in Metabolism (NUTRIM), Maastricht University, P.O. Box 616, 6200 MD Maastricht, The Netherlands; (A.M.); (R.W.L.G.)
| | - Roger W. L. Godschalk
- Department of Pharmacology and Toxicology, School for Nutrition and Translational Research in Metabolism (NUTRIM), Maastricht University, P.O. Box 616, 6200 MD Maastricht, The Netherlands; (A.M.); (R.W.L.G.)
| | - Sabine A. S. Langie
- Department of Pharmacology and Toxicology, School for Nutrition and Translational Research in Metabolism (NUTRIM), Maastricht University, P.O. Box 616, 6200 MD Maastricht, The Netherlands; (A.M.); (R.W.L.G.)
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6
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Solta A, Boettiger K, Kovács I, Lang C, Megyesfalvi Z, Ferk F, Mišík M, Hoetzenecker K, Aigner C, Kowol CR, Knasmueller S, Grusch M, Szeitz B, Rezeli M, Dome B, Schelch K. Entinostat Enhances the Efficacy of Chemotherapy in Small Cell Lung Cancer Through S-phase Arrest and Decreased Base Excision Repair. Clin Cancer Res 2023; 29:4644-4659. [PMID: 37725585 PMCID: PMC10644001 DOI: 10.1158/1078-0432.ccr-23-1795] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2023] [Revised: 08/10/2023] [Accepted: 09/13/2023] [Indexed: 09/21/2023]
Abstract
PURPOSE Acquired chemoresistance is a frequent event in small cell lung cancer (SCLC), one of the deadliest human malignancies. Histone deacetylase inhibitors (HDACi) have been shown to synergize with different chemotherapeutic agents including cisplatin. Accordingly, we aimed to investigate the dual targeting of HDAC inhibition and chemotherapy in SCLC. EXPERIMENTAL DESIGN The efficacy of HDACi and chemotherapy in SCLC was investigated both in vitro and in vivo. Synergistic drug interactions were calculated based on the HSA model (Combenefit software). Results from the proteomic analysis were confirmed via ICP-MS, cell-cycle analysis, and comet assays. RESULTS Single entinostat- or chemotherapy significantly reduced cell viability in human neuroendocrine SCLC cells. The combination of entinostat with either cisplatin, carboplatin, irinotecan, epirubicin, or etoposide led to strong synergy in a subset of resistant SCLC cells. Combination treatment with entinostat and cisplatin significantly decreased tumor growth in vivo. Proteomic analysis comparing the groups of SCLC cell lines with synergistic and additive response patterns indicated alterations in cell-cycle regulation and DNA damage repair. Cell-cycle analysis revealed that cells exhibiting synergistic drug responses displayed a shift from G1 to S-phase compared with cells showing additive features upon dual treatment. Comet assays demonstrated more DNA damage and decreased base excision repair in SCLC cells more responsive to combination therapy. CONCLUSIONS In this study, we decipher the molecular processes behind synergistic interactions between chemotherapy and HDAC inhibition. Moreover, we report novel mechanisms to overcome drug resistance in SCLC, which may be relevant to increasing therapeutic success.
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Affiliation(s)
- Anna Solta
- Department of Thoracic Surgery, Comprehensive Cancer Center, Medical University of Vienna, Vienna, Austria
| | - Kristiina Boettiger
- Department of Thoracic Surgery, Comprehensive Cancer Center, Medical University of Vienna, Vienna, Austria
| | - Ildikó Kovács
- National Koranyi Institute of Pulmonology, Budapest, Hungary
| | - Christian Lang
- Department of Thoracic Surgery, Comprehensive Cancer Center, Medical University of Vienna, Vienna, Austria
- Division of Pulmonology, Department of Medicine II, Medical University of Vienna, Austria
| | - Zsolt Megyesfalvi
- Department of Thoracic Surgery, Comprehensive Cancer Center, Medical University of Vienna, Vienna, Austria
- National Koranyi Institute of Pulmonology, Budapest, Hungary
- Department of Thoracic Surgery, Semmelweis University and National Institute of Oncology, Budapest, Hungary
| | - Franziska Ferk
- Center for Cancer Research, Medical University Vienna, Vienna, Austria
| | - Miroslav Mišík
- Center for Cancer Research, Medical University Vienna, Vienna, Austria
| | - Konrad Hoetzenecker
- Department of Thoracic Surgery, Comprehensive Cancer Center, Medical University of Vienna, Vienna, Austria
| | - Clemens Aigner
- Department of Thoracic Surgery, Comprehensive Cancer Center, Medical University of Vienna, Vienna, Austria
| | - Christian R. Kowol
- Institute of Inorganic Chemistry, Faculty of Chemistry, University of Vienna, Vienna, Austria
| | | | - Michael Grusch
- Center for Cancer Research, Medical University Vienna, Vienna, Austria
| | - Beáta Szeitz
- Division of Oncology, Department of Internal Medicine and Oncology, Semmelweis University, Budapest, Hungary
| | - Melinda Rezeli
- Department of Biomedical Engineering, Lund University, Lund, Sweden
| | - Balazs Dome
- Department of Thoracic Surgery, Comprehensive Cancer Center, Medical University of Vienna, Vienna, Austria
- National Koranyi Institute of Pulmonology, Budapest, Hungary
- Department of Thoracic Surgery, Semmelweis University and National Institute of Oncology, Budapest, Hungary
- Department of Translational Medicine, Lund University, Lund, Sweden
| | - Karin Schelch
- Department of Thoracic Surgery, Comprehensive Cancer Center, Medical University of Vienna, Vienna, Austria
- Center for Cancer Research, Medical University Vienna, Vienna, Austria
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Popov AA, Petruseva IO, Naumenko NV, Lavrik OI. Methods for Assessment of Nucleotide Excision Repair Efficiency. BIOCHEMISTRY. BIOKHIMIIA 2023; 88:1844-1856. [PMID: 38105203 DOI: 10.1134/s0006297923110147] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/29/2023] [Revised: 08/30/2023] [Accepted: 08/31/2023] [Indexed: 12/19/2023]
Abstract
Nucleotide excision repair (NER) is responsible for removing a wide variety of bulky adducts from DNA, thus contributing to the maintenance of genome stability. The efficiency with which proteins of the NER system recognize and remove bulky adducts depends on many factors and is of great clinical and diagnostic significance. The review examines current concepts of the NER system molecular basis in eukaryotic cells and analyzes methods for the assessment of the NER-mediated DNA repair efficiency both in vitro and ex vivo.
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Affiliation(s)
- Aleksei A Popov
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, 630090, Russia
| | - Irina O Petruseva
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, 630090, Russia
| | - Natalya V Naumenko
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, 630090, Russia
| | - Olga I Lavrik
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, 630090, Russia.
- Novosibirsk National Research State University, Novosibirsk, 630090, Russia
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8
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Møller P, Azqueta A, Rodriguez-Garraus A, Bakuradze T, Richling E, Bankoglu EE, Stopper H, Claudino Bastos V, Langie SAS, Jensen A, Ristori S, Scavone F, Giovannelli L, Wojewódzka M, Kruszewski M, Valdiglesias V, Laffon B, Costa C, Costa S, Paulo Teixeira J, Marino M, Del Bo' C, Riso P, Zheng C, Shaposhnikov S, Collins A. Long-term cryopreservation of potassium bromate positive assay controls for measurement of oxidatively damaged DNA by the Fpg-modified comet assay: results from the hCOMET ring trial. Mutagenesis 2023; 38:264-272. [PMID: 37357815 DOI: 10.1093/mutage/gead020] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2023] [Accepted: 06/23/2023] [Indexed: 06/27/2023] Open
Abstract
The formamidopyrimidine DNA glycosylase (Fpg)-modified comet assay is widely used for the measurement of oxidatively generated damage to DNA. However, there has not been a recommended long-term positive control for this version of the comet assay. We have investigated potassium bromate as a positive control for the Fpg-modified comet assay because it generates many Fpg-sensitive sites with a little concurrent generation of DNA strand breaks. Eight laboratories used the same procedure for the treatment of monocytic THP-1 cells with potassium bromate (0, 0.5, 1.5, and 4.5 mM) and subsequent cryopreservation in a freezing medium consisting of 50% foetal bovine serum, 40% RPMI-1640 medium, and 10% dimethyl sulphoxide. The samples were analysed by the Fpg-modified comet assay three times over a 3-year period. All laboratories obtained a positive concentration-response relationship in cryopreserved samples (linear regression coefficients ranging from 0.79 to 0.99). However, there was a wide difference in the levels of Fpg-sensitive sites between the laboratory with the lowest (4.2% Tail DNA) and highest (74% Tail DNA) values in THP-1 cells after exposure to 4.5 mM KBrO3. In an attempt to assess sources of inter-laboratory variation in Fpg-sensitive sites, comet images from one experiment in each laboratory were forwarded to a central laboratory for visual scoring. There was high consistency between measurements of %Tail DNA values in each laboratory and the visual score of the same comets done in the central laboratory (r = 0.98, P < 0.001, linear regression). In conclusion, the results show that potassium bromate is a suitable positive comet assay control.
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Affiliation(s)
- Peter Møller
- Department of Public Health, Section of Environmental Health, University of Copenhagen, Øster Farimagsgade 5A, DK-1014 Copenhagen K, Denmark
| | - Amaya Azqueta
- Department of Pharmacology and Toxicology, School of Pharmacy and Nutrition, University of Navarra, C/Irunlarrea 1, 31009 Pamplona, Spain
| | - Adriana Rodriguez-Garraus
- Department of Pharmacology and Toxicology, School of Pharmacy and Nutrition, University of Navarra, C/Irunlarrea 1, 31009 Pamplona, Spain
| | - Tamara Bakuradze
- Food Chemistry and Toxicology, Department of Chemistry, Rhineland-Palatinate Technical University Kaiserslautern-Landau, Erwin-Schroedinger-Str. 52, D-67663 Kaiserslautern, Germany
| | - Elke Richling
- Food Chemistry and Toxicology, Department of Chemistry, Rhineland-Palatinate Technical University Kaiserslautern-Landau, Erwin-Schroedinger-Str. 52, D-67663 Kaiserslautern, Germany
| | - Ezgi Eyluel Bankoglu
- Institute of Pharmacology and Toxicology, University of Wuerzburg, Versbacher Str. 9, 97078 Wuerzburg, Germany
| | - Helga Stopper
- Institute of Pharmacology and Toxicology, University of Wuerzburg, Versbacher Str. 9, 97078 Wuerzburg, Germany
| | - Victoria Claudino Bastos
- Department of Pharmacology and Toxicology, School for Nutrition and Translational Research in Metabolism (NUTRIM), Maastricht University, Maastricht, The Netherlands
| | - Sabine A S Langie
- Department of Pharmacology and Toxicology, School for Nutrition and Translational Research in Metabolism (NUTRIM), Maastricht University, Maastricht, The Netherlands
| | - Annie Jensen
- Department of Public Health, Section of Environmental Health, University of Copenhagen, Øster Farimagsgade 5A, DK-1014 Copenhagen K, Denmark
| | - Sara Ristori
- Department of Neuroscience, Psychology, Pharmacology and Child Health (NEUROFARBA), Section Pharmacology and Toxicology, University of Florence, Florence, Italy
| | - Francesca Scavone
- Department of Neuroscience, Psychology, Pharmacology and Child Health (NEUROFARBA), Section Pharmacology and Toxicology, University of Florence, Florence, Italy
| | - Lisa Giovannelli
- Department of Neuroscience, Psychology, Pharmacology and Child Health (NEUROFARBA), Section Pharmacology and Toxicology, University of Florence, Florence, Italy
| | - Maria Wojewódzka
- Centre for Radiobiology and Biological Dosimetry, Institute of Nuclear Chemistry and Technology, Dorodna 16, 01-310 Warsaw, Poland
| | - Marcin Kruszewski
- Centre for Radiobiology and Biological Dosimetry, Institute of Nuclear Chemistry and Technology, Dorodna 16, 01-310 Warsaw, Poland
- Department of Molecular Biology and Translational Research, Institute of Rural Health, Jaczewskiego 2, 20-090 Lublin, Poland
| | - Vanessa Valdiglesias
- Universidade da Coruña, Grupo NanoToxGen, Centro Interdisciplinar de Química e Bioloxía - CICA, Departamento de Biología, A Coruña, Spain
- Instituto de Investigación Biomédica de A Coruña (INIBIC), A Coruña, Spain
| | - Blanca Laffon
- Instituto de Investigación Biomédica de A Coruña (INIBIC), A Coruña, Spain
- Universidade da Coruña, Grupo DICOMOSA, Centro Interdisciplinar de Química e Bioloxía - CICA, Departamento de Psicología, A Coruña, Spain
| | - Carla Costa
- Environmental Health Department, National Institute of Health, Porto, Portugal
- EPIUnit-Instituto de Saúde Pública, Universidade do Porto, Porto, Portugal
- Laboratory for Integrative and Translational Research in Population Health (ITR), Porto, Portugal
| | - Solange Costa
- Environmental Health Department, National Institute of Health, Porto, Portugal
- EPIUnit-Instituto de Saúde Pública, Universidade do Porto, Porto, Portugal
- Laboratory for Integrative and Translational Research in Population Health (ITR), Porto, Portugal
| | - João Paulo Teixeira
- Environmental Health Department, National Institute of Health, Porto, Portugal
- EPIUnit-Instituto de Saúde Pública, Universidade do Porto, Porto, Portugal
- Laboratory for Integrative and Translational Research in Population Health (ITR), Porto, Portugal
| | - Mirko Marino
- Department of Food, Environmental and Nutritional Sciences (DeFENS), Università degli Studi di Milano, 20133 Milan, Italy
| | - Cristian Del Bo'
- Department of Food, Environmental and Nutritional Sciences (DeFENS), Università degli Studi di Milano, 20133 Milan, Italy
| | - Patrizia Riso
- Department of Food, Environmental and Nutritional Sciences (DeFENS), Università degli Studi di Milano, 20133 Milan, Italy
| | - Congying Zheng
- Department of Pharmacology and Toxicology, School for Nutrition and Translational Research in Metabolism (NUTRIM), Maastricht University, Maastricht, The Netherlands
- Department of Nutrition, University of Oslo, Norway
| | | | - Andrew Collins
- Department of Nutrition, University of Oslo, Norway
- NorGenotech AS, Oslo, Norway
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9
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Møller P, Azqueta A, Rodriguez-Garraus A, Bakuradze T, Richling E, Bankoglu EE, Stopper H, Claudino Bastos V, Langie SAS, Jensen A, Ristori S, Scavone F, Giovannelli L, Wojewódzka M, Kruszewski M, Valdiglesias V, Laffon B, Costa C, Costa S, Paulo Teixeira J, Marino M, Del Bo C, Riso P, Zheng C, Shaposhnikov S, Collins A. DNA strand break levels in cryopreserved mononuclear blood cell lines measured by the alkaline comet assay: results from the hCOMET ring trial. Mutagenesis 2023; 38:273-282. [PMID: 37357800 DOI: 10.1093/mutage/gead019] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2023] [Accepted: 06/23/2023] [Indexed: 06/27/2023] Open
Abstract
The comet assay is widely used in biomonitoring studies for the analysis of DNA damage in leukocytes and peripheral blood mononuclear cells. Rather than processing blood samples directly, it can be desirable to cryopreserve whole blood or isolated cells for later analysis by the comet assay. However, this creates concern about artificial accumulation of DNA damage during cryopreservation. In this study, 10 laboratories used standardized cryopreservation and thawing procedures of monocytic (THP-1) or lymphocytic (TK6) cells. Samples were cryopreserved in small aliquots in 50% foetal bovine serum, 40% cell culture medium, and 10% dimethyl sulphoxide. Subsequently, cryopreserved samples were analysed by the standard comet assay on three occasions over a 3-year period. Levels of DNA strand breaks in THP-1 cells were increased (four laboratories), unaltered (four laboratories), or decreased (two laboratories) by long-term storage. Pooled analysis indicates only a modest positive association between storage time and levels of DNA strand breaks in THP-1 cells (0.37% Tail DNA per year, 95% confidence interval: -0.05, 0.78). In contrast, DNA strand break levels were not increased by cryopreservation in TK6 cells. There was inter-laboratory variation in levels of DNA strand breaks in THP-1 cells (SD = 3.7% Tail DNA) and TK6 reference sample cells (SD = 9.4% Tail DNA), whereas the intra-laboratory residual variation was substantially smaller (i.e. SD = 0.4%-2.2% Tail DNA in laboratories with the smallest and largest variation). In conclusion, the study shows that accumulation of DNA strand breaks in cryopreserved mononuclear blood cell lines is not a matter of concern.
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Affiliation(s)
- Peter Møller
- Department of Public Health, Section of Environmental Health, University of Copenhagen, Øster Farimagsgade 5A, DK-1014 Copenhagen K, Denmark
| | - Amaya Azqueta
- Department of Pharmacology and Toxicology, School of Pharmacy and Nutrition, University of Navarra, C/Irunlarrea 1, 31009 Pamplona, Spain
| | - Adriana Rodriguez-Garraus
- Department of Pharmacology and Toxicology, School of Pharmacy and Nutrition, University of Navarra, C/Irunlarrea 1, 31009 Pamplona, Spain
| | - Tamara Bakuradze
- Food Chemistry and Toxicology, Department of Chemistry, RPTU Kaiserslautern-Landau, Erwin-Schroedinger-Str. 52, D-67663 Kaiserslautern, Germany
| | - Elke Richling
- Food Chemistry and Toxicology, Department of Chemistry, RPTU Kaiserslautern-Landau, Erwin-Schroedinger-Str. 52, D-67663 Kaiserslautern, Germany
| | - Ezgi Eyluel Bankoglu
- Institute of Pharmacology and Toxicology, University of Wuerzburg, Versbacher Str. 9, 97078 Wuerzburg, Germany
| | - Helga Stopper
- Institute of Pharmacology and Toxicology, University of Wuerzburg, Versbacher Str. 9, 97078 Wuerzburg, Germany
| | - Victoria Claudino Bastos
- Department of Pharmacology & Toxicology, School for Nutrition and Translational Research in Metabolism (NUTRIM), Maastricht University, Maastricht, The Netherlands
| | - Sabine A S Langie
- Department of Pharmacology & Toxicology, School for Nutrition and Translational Research in Metabolism (NUTRIM), Maastricht University, Maastricht, The Netherlands
| | - Annie Jensen
- Department of Public Health, Section of Environmental Health, University of Copenhagen, Øster Farimagsgade 5A, DK-1014 Copenhagen K, Denmark
| | - Sara Ristori
- Department of Neuroscience, Psychology, Pharmacology and Child Health (NEUROFARBA), Section Pharmacology and Toxicology, University of Florence, Florence, Italy
| | - Francesca Scavone
- Department of Neuroscience, Psychology, Pharmacology and Child Health (NEUROFARBA), Section Pharmacology and Toxicology, University of Florence, Florence, Italy
| | - Lisa Giovannelli
- Department of Neuroscience, Psychology, Pharmacology and Child Health (NEUROFARBA), Section Pharmacology and Toxicology, University of Florence, Florence, Italy
| | - Maria Wojewódzka
- Centre for Radiobiology and Biological Dosimetry, Institute of Nuclear Chemistry and Technology, Dorodna 16, 01-310 Warsaw, Poland
| | - Marcin Kruszewski
- Centre for Radiobiology and Biological Dosimetry, Institute of Nuclear Chemistry and Technology, Dorodna 16, 01-310 Warsaw, Poland
- Department of Molecular Biology and Translational Research, Institute of Rural Health, Jaczewskiego 2, 20-090 Lublin, Poland
| | - Vanessa Valdiglesias
- Universidade da Coruña, Grupo NanoToxGen, Centro Interdisciplinar de Química e Bioloxía - CICA, Departamento de Biología, A Coruña, Spain
- Instituto de Investigación Biomédica de A Coruña (INIBIC), A Coruña, Spain
| | - Blanca Laffon
- Instituto de Investigación Biomédica de A Coruña (INIBIC), A Coruña, Spain
- Universidade da Coruña, Grupo DICOMOSA, Centro Interdisciplinar de Química e Bioloxía - CICA, Departamento de Psicología, A Coruña, Spain
| | - Carla Costa
- Environmental Health Department, National Institute of Health, Porto, Portugal
- EPIUnit - Instituto de Saúde Pública, Universidade do Porto, Porto, Portugal
- Laboratory for Integrative and Translational Research in Population Health (ITR), Porto, Portugal
| | - Solange Costa
- Environmental Health Department, National Institute of Health, Porto, Portugal
- EPIUnit - Instituto de Saúde Pública, Universidade do Porto, Porto, Portugal
- Laboratory for Integrative and Translational Research in Population Health (ITR), Porto, Portugal
| | - João Paulo Teixeira
- Environmental Health Department, National Institute of Health, Porto, Portugal
- EPIUnit - Instituto de Saúde Pública, Universidade do Porto, Porto, Portugal
- Laboratory for Integrative and Translational Research in Population Health (ITR), Porto, Portugal
| | - Mirko Marino
- Department of Food, Environmental and Nutritional Sciences (DeFENS), Università degli Studi di Milano, 20133 Milan, Italy
| | - Cristian Del Bo
- Department of Food, Environmental and Nutritional Sciences (DeFENS), Università degli Studi di Milano, 20133 Milan, Italy
| | - Patrizia Riso
- Department of Food, Environmental and Nutritional Sciences (DeFENS), Università degli Studi di Milano, 20133 Milan, Italy
| | - Congying Zheng
- Department of Pharmacology & Toxicology, School for Nutrition and Translational Research in Metabolism (NUTRIM), Maastricht University, Maastricht, The Netherlands
- Department of Nutrition, University of Oslo, Oslo, Norway
| | | | - Andrew Collins
- Department of Nutrition, University of Oslo, Oslo, Norway
- NorGenotech AS, Oslo, Norway
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10
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Møller P, Azqueta A, Collia M, Bakuradze T, Richling E, Bankoglu EE, Stopper H, Bastos VC, Langie SAS, Jensen A, Ristori S, Scavone F, Giovannelli L, Wojewódzka M, Kruszewski M, Valdiglesias V, Laffon B, Costa C, Costa S, Teixeira JP, Marino M, Del Bo C, Riso P, Zheng C, Shaposhnikov S, Collins A. Inter-laboratory variation in measurement of DNA damage by the alkaline comet assay in the hCOMET ring trial. Mutagenesis 2023; 38:283-294. [PMID: 37228081 DOI: 10.1093/mutage/gead014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2023] [Accepted: 05/23/2023] [Indexed: 05/27/2023] Open
Abstract
The comet assay is a simple and versatile method for measurement of DNA damage in eukaryotic cells. More specifically, the assay detects DNA migration from agarose gel-embedded nucleoids, which depends on assay conditions and the level of DNA damage. Certain steps in the comet assay procedure have substantial impact on the magnitude of DNA migration (e.g. electric potential and time of electrophoresis). Inter-laboratory variation in DNA migration levels occurs because there is no agreement on optimal assay conditions or suitable assay controls. The purpose of the hCOMET ring trial was to test potassium bromate (KBrO3) as a positive control for the formamidopyrimidine DNA glycosylase (Fpg)-modified comet assay. To this end, participating laboratories used semi-standardized protocols for cell culture (i.e. cell culture, KBrO3 exposure, and cryopreservation of cells) and comet assay procedures, whereas the data acquisition was not standardized (i.e. staining of comets and image analysis). Segregation of the total variation into partial standard deviation (SD) in % Tail DNA units indicates the importance of cell culture procedures (SD = 10.9), comet assay procedures (SD = 12.3), staining (SD = 7.9) and image analysis (SD = 0.5) on the overall inter-laboratory variation of DNA migration (SD = 18.2). Future studies should assess sources of variation in each of these steps. On the positive side, the hCOMET ring trial demonstrates that KBrO3 is a robust positive control for the Fpg-modified comet assay. In conclusion, the hCOMET ring trial has demonstrated a high reproducibility of detecting genotoxic effects by the comet assay, but inter-laboratory variation of DNA migration levels is a concern.
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Affiliation(s)
- Peter Møller
- Department of Public Health, Section of Environmental Health, University of Copenhagen, Øster Farimagsgade 5A, DK-1014 Copenhagen K, Denmark
| | - Amaya Azqueta
- Department of Pharmacology and Toxicology, School of Pharmacy and Nutrition. University of Navarra, C/Irunlarrea 1, 31009 Pamplona, Spain
| | - Miguel Collia
- Department of Pharmacology and Toxicology, School of Pharmacy and Nutrition. University of Navarra, C/Irunlarrea 1, 31009 Pamplona, Spain
| | - Tamara Bakuradze
- Food Chemistry and Toxicology, Department of Chemistry, RPTU Kaiserslautern-Landau, Erwin-Schroedinger-Str. 52, D-67663 Kaiserslautern, Germany
| | - Elke Richling
- Food Chemistry and Toxicology, Department of Chemistry, RPTU Kaiserslautern-Landau, Erwin-Schroedinger-Str. 52, D-67663 Kaiserslautern, Germany
| | - Ezgi Eyluel Bankoglu
- Institute of Pharmacology and Toxicology, University of Wuerzburg, Versbacher Str. 9, 97078 Wuerzburg, Germany
| | - Helga Stopper
- Institute of Pharmacology and Toxicology, University of Wuerzburg, Versbacher Str. 9, 97078 Wuerzburg, Germany
| | - Victoria Claudino Bastos
- Department of Pharmacology & Toxicology, School for Nutrition and Translational Research in Metabolism (NUTRIM), Maastricht University, Maastricht, The Netherlands
| | - Sabine A S Langie
- Department of Pharmacology & Toxicology, School for Nutrition and Translational Research in Metabolism (NUTRIM), Maastricht University, Maastricht, The Netherlands
| | - Annie Jensen
- Department of Public Health, Section of Environmental Health, University of Copenhagen, Øster Farimagsgade 5A, DK-1014 Copenhagen K, Denmark
| | - Sara Ristori
- Department of Neuroscience, Psychology, Pharmacology and Child Health (NEUROFARBA), Section Pharmacology and Toxicology, University of Florence, Florence, Italy
| | - Francesca Scavone
- Department of Neuroscience, Psychology, Pharmacology and Child Health (NEUROFARBA), Section Pharmacology and Toxicology, University of Florence, Florence, Italy
| | - Lisa Giovannelli
- Department of Neuroscience, Psychology, Pharmacology and Child Health (NEUROFARBA), Section Pharmacology and Toxicology, University of Florence, Florence, Italy
| | - Maria Wojewódzka
- Centre for Radiobiology and Biological Dosimetry, Institute of Nuclear Chemistry and Technology, Dorodna 16, 01-310 Warsaw, Poland
| | - Marcin Kruszewski
- Centre for Radiobiology and Biological Dosimetry, Institute of Nuclear Chemistry and Technology, Dorodna 16, 01-310 Warsaw, Poland
- Department of Molecular Biology and Translational Research, Institute of Rural Health, Jaczewskiego 2, 20-090 Lublin, Poland
| | - Vanessa Valdiglesias
- Universidade da Coruña, Grupo NanoToxGen, Centro Interdisciplinar de Química e Bioloxía - CICA, Departamento de Biología, A Coruña, Spain
- Instituto de Investigación Biomédica de A Coruña (INIBIC), A Coruña, Spain
| | - Blanca Laffon
- Instituto de Investigación Biomédica de A Coruña (INIBIC), A Coruña, Spain
- Universidade da Coruña, Grupo DICOMOSA, Centro Interdisciplinar de Química e Bioloxía - CICA, Departamento de Psicología, A Coruña, Spain
| | - Carla Costa
- Environmental Health Department, National Institute of Health, Porto, Portugal
- EPIUnit - Instituto de Saúde Pública, Universidade do Porto, Porto, Portugal
- Laboratory for Integrative and Translational Research in Population Health (ITR), Porto, Portugal
| | - Solange Costa
- Environmental Health Department, National Institute of Health, Porto, Portugal
- EPIUnit - Instituto de Saúde Pública, Universidade do Porto, Porto, Portugal
- Laboratory for Integrative and Translational Research in Population Health (ITR), Porto, Portugal
| | - João Paulo Teixeira
- Environmental Health Department, National Institute of Health, Porto, Portugal
- EPIUnit - Instituto de Saúde Pública, Universidade do Porto, Porto, Portugal
- Laboratory for Integrative and Translational Research in Population Health (ITR), Porto, Portugal
| | - Mirko Marino
- Department of Food, Environmental and Nutritional Sciences (DeFENS), Università degli Studi di Milano, 20133 Milan, Italy
| | - Cristian Del Bo
- Department of Food, Environmental and Nutritional Sciences (DeFENS), Università degli Studi di Milano, 20133 Milan, Italy
| | - Patrizia Riso
- Department of Food, Environmental and Nutritional Sciences (DeFENS), Università degli Studi di Milano, 20133 Milan, Italy
| | - Congying Zheng
- Department of Pharmacology & Toxicology, School for Nutrition and Translational Research in Metabolism (NUTRIM), Maastricht University, Maastricht, The Netherlands
- Department of Nutrition, University of Oslo, Oslo, Norway
| | | | - Andrew Collins
- Department of Nutrition, University of Oslo, Oslo, Norway
- NorGenotech AS, Oslo, Norway
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11
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Møller P, Azqueta A, Sanz-Serrano J, Bakuradze T, Richling E, Eyluel Bankoglu E, Stopper H, Claudino Bastos V, Langie SAS, Jensen A, Scavone F, Giovannelli L, Wojewódzka M, Kruszewski M, Valdiglesias V, Laffon B, Costa C, Costa S, Teixeira JP, Marino M, Del Bo C, Riso P, Zheng C, Shaposhnikov S, Collins A. Visual comet scoring revisited: a guide to scoring comet assay slides and obtaining reliable results. Mutagenesis 2023; 38:253-263. [PMID: 37233347 DOI: 10.1093/mutage/gead015] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2023] [Accepted: 05/23/2023] [Indexed: 05/27/2023] Open
Abstract
Measurement of DNA migration in the comet assay can be done by image analysis or visual scoring. The latter accounts for 20%-25% of the published comet assay results. Here we assess the intra- and inter-investigator variability in visual scoring of comets. We include three training sets of comet images, which can be used as reference for researchers who wish to use visual scoring of comets. Investigators in 11 different laboratories scored the comet images using a five-class scoring system. There is inter-investigator variation in the three training sets of comets (i.e. coefficient of variation (CV) = 9.7%, 19.8%, and 15.2% in training sets I-III, respectively). However, there is also a positive correlation of inter-investigator scoring in the three training sets (r = 0.60). Overall, 36% of the variation is attributed to inter-investigator variation and 64% stems from intra-investigator variation in scoring between comets (i.e. the comets in training sets I-III look slightly different and this gives rise to heterogeneity in scoring). Intra-investigator variation in scoring was also assessed by repeated analysis of the training sets by the same investigator. There was larger variation when the training sets were scored over a period of six months (CV = 5.9%-9.6%) as compared to 1 week (CV = 1.3%-6.1%). A subsequent study revealed a high inter-investigator variation when premade slides, prepared in a central laboratory, were stained and scored by investigators in different laboratories (CV = 105% and 18%-20% in premade slides with comets from unexposed and hydrogen peroxide-exposed cells, respectively). The results indicate that further standardization of visual scoring is desirable. Nevertheless, the analysis demonstrates that visual scoring is a reliable way of analysing DNA migration in comets.
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Affiliation(s)
- Peter Møller
- Department of Public Health, Section of Environmental Health, University of Copenhagen, Øster Farimagsgade 5A, DK-1014 Copenhagen K, Denmark
| | - Amaya Azqueta
- Department of Pharmacology and Toxicology, School of Pharmacy and Nutrition. University of Navarra, C/Irunlarrea 1, 31009 Pamplona, Spain
| | - Julen Sanz-Serrano
- Department of Pharmacology and Toxicology, School of Pharmacy and Nutrition. University of Navarra, C/Irunlarrea 1, 31009 Pamplona, Spain
| | - Tamara Bakuradze
- Food Chemistry and Toxicology, Department of Chemistry, RPTU Kaiserslautern-Landau, Erwin-Schroedinger-Str. 52, D-67663 Kaiserslautern, Germany
| | - Elke Richling
- Food Chemistry and Toxicology, Department of Chemistry, RPTU Kaiserslautern-Landau, Erwin-Schroedinger-Str. 52, D-67663 Kaiserslautern, Germany
| | - Ezgi Eyluel Bankoglu
- Institute of Pharmacology and Toxicology, University of Würzburg, Versbacher Str. 9, 97078 Wuerzburg, Germany
| | - Helga Stopper
- Institute of Pharmacology and Toxicology, University of Würzburg, Versbacher Str. 9, 97078 Wuerzburg, Germany
| | - Victoria Claudino Bastos
- Department of Pharmacology & Toxicology, School for Nutrition and Translational Research in Metabolism (NUTRIM), Maastricht University, Maastricht, The Netherlands
| | - Sabine A S Langie
- Department of Pharmacology & Toxicology, School for Nutrition and Translational Research in Metabolism (NUTRIM), Maastricht University, Maastricht, The Netherlands
| | - Annie Jensen
- Department of Public Health, Section of Environmental Health, University of Copenhagen, Øster Farimagsgade 5A, DK-1014 Copenhagen K, Denmark
| | - Francesca Scavone
- Department of Neuroscience, Psychology, Pharmacology and Child Health (NEUROFARBA), Section Pharmacology and Toxicology, University of Florence, Florence, Italy
| | - Lisa Giovannelli
- Department of Neuroscience, Psychology, Pharmacology and Child Health (NEUROFARBA), Section Pharmacology and Toxicology, University of Florence, Florence, Italy
| | - Maria Wojewódzka
- Centre for Radiobiology and Biological Dosimetry, Institute of Nuclear Chemistry and Technology, Dorodna 16, 01-310 Warsaw, Poland
| | - Marcin Kruszewski
- Centre for Radiobiology and Biological Dosimetry, Institute of Nuclear Chemistry and Technology, Dorodna 16, 01-310 Warsaw, Poland
- Department of Molecular Biology and Translational Research, Institute of Rural Health, Jaczewskiego 2, 20-090 Lublin, Poland
| | - Vanessa Valdiglesias
- Universidade da Coruña, Grupo NanoToxGen, Centro Interdisciplinar de Química e Bioloxía - CICA, Departamento de Biología, A Coruña, Spain
- Instituto de Investigación Biomédica de A Coruña (INIBIC), A Coruña, Spain
| | - Blanca Laffon
- Instituto de Investigación Biomédica de A Coruña (INIBIC), A Coruña, Spain
- Universidade da Coruña, Grupo DICOMOSA, Centro Interdisciplinar de Química e Bioloxía - CICA, Departamento de Psicología, A Coruña, Spain
| | - Carla Costa
- Environmental Health Department, National Institute of Health, Porto, Portugal
- EPIUnit - Instituto de Saúde Pública, Universidade do Porto, Porto, Portugal
- Laboratory for Integrative and Translational Research in Population Health (ITR), Porto, Portugal
| | - Solange Costa
- Environmental Health Department, National Institute of Health, Porto, Portugal
- EPIUnit - Instituto de Saúde Pública, Universidade do Porto, Porto, Portugal
- Laboratory for Integrative and Translational Research in Population Health (ITR), Porto, Portugal
| | - João Paulo Teixeira
- Environmental Health Department, National Institute of Health, Porto, Portugal
- EPIUnit - Instituto de Saúde Pública, Universidade do Porto, Porto, Portugal
- Laboratory for Integrative and Translational Research in Population Health (ITR), Porto, Portugal
| | - Mirko Marino
- Department of Food, Environmental and Nutritional Sciences (DeFENS), Università degli Studi di Milano, 20133 Milan, Italy
| | - Cristian Del Bo
- Department of Food, Environmental and Nutritional Sciences (DeFENS), Università degli Studi di Milano, 20133 Milan, Italy
| | - Patrizia Riso
- Department of Food, Environmental and Nutritional Sciences (DeFENS), Università degli Studi di Milano, 20133 Milan, Italy
| | - Congying Zheng
- Department of Pharmacology & Toxicology, School for Nutrition and Translational Research in Metabolism (NUTRIM), Maastricht University, Maastricht, The Netherlands
- NorGenotech AS, Oslo, Norway
| | | | - Andrew Collins
- NorGenotech AS, Oslo, Norway
- Department of Nutrition, University of Oslo, Oslo, Norway
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12
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Zheng C, Shaposhnikov S, Collins A, Brunborg G, Oancea F, Van Schooten FJ, Godschalk R. Comparison of comet-based approaches to assess base excision repair. Arch Toxicol 2023; 97:2273-2281. [PMID: 37349528 PMCID: PMC10322757 DOI: 10.1007/s00204-023-03543-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2023] [Accepted: 06/06/2023] [Indexed: 06/24/2023]
Abstract
DNA repair plays an essential role in maintaining genomic stability, and can be assessed by various comet assay-based approaches, including the cellular repair assay and the in vitro repair assay. In the cellular repair assay, cells are challenged with a DNA-damaging compound and DNA damage removal over time is assessed. In the in vitro repair assay, an early step in the repair process is assessed as the ability of a cellular extract to recognize and incise damaged DNA in substrate nucleoids from cells treated with a DNA-damaging compound. Our direct comparison of both assays in eight cell lines and human peripheral blood lymphocytes indicated no significant relationship between these DNA repair assays (R2 = 0.084, P = 0.52). The DNA incision activity of test cells measured with the in vitro repair assay correlated with the background level of DNA damage in the untreated test cells (R2 = 0.621, P = 0.012). When extracts were prepared from cells exposed to DNA-damaging agents (10 mM KBrO3 or 1 µM Ro 19-8022 plus light), the incision activity was significantly increased, which is in line with the notion that base excision repair is inducible. The data presented suggest that the two assays do not measure the same endpoint of DNA repair and should be considered as complementary.
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Affiliation(s)
- Congying Zheng
- Department of Pharmacology and Toxicology, NUTRIM School of Nutrition and Translational Research in Metabolism, Maastricht University, 6200, Maastricht, Netherlands
- Norgenotech AS, 64/66, 0379, Ullernchassern, Oslo, Norway
- Oslo Cancer Cluster, 64/66, 0379, Ullernchausseen, Oslo, Norway
| | - Sergey Shaposhnikov
- Norgenotech AS, 64/66, 0379, Ullernchassern, Oslo, Norway
- Oslo Cancer Cluster, 64/66, 0379, Ullernchausseen, Oslo, Norway
| | - Andrew Collins
- Norgenotech AS, 64/66, 0379, Ullernchassern, Oslo, Norway
| | | | - Florin Oancea
- National Institute for Research & Development in Chemistry and Petrochemistry, Splaiul Independenței 202, București, Romania
| | - Frederik-Jan Van Schooten
- Department of Pharmacology and Toxicology, NUTRIM School of Nutrition and Translational Research in Metabolism, Maastricht University, 6200, Maastricht, Netherlands
| | - Roger Godschalk
- Department of Pharmacology and Toxicology, NUTRIM School of Nutrition and Translational Research in Metabolism, Maastricht University, 6200, Maastricht, Netherlands.
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Rodríguez R, Gaivão I, Aguado L, Espina M, García J, Martínez-Camblor P, Sierra LM. The Comet Assay in Drosophila: A Tool to Study Interactions between DNA Repair Systems in DNA Damage Responses In Vivo and Ex Vivo. Cells 2023; 12:1979. [PMID: 37566058 PMCID: PMC10417035 DOI: 10.3390/cells12151979] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2023] [Revised: 07/26/2023] [Accepted: 07/30/2023] [Indexed: 08/12/2023] Open
Abstract
The comet assay in Drosophila has been used in the last few years to study DNA damage responses (DDR) in different repair-mutant strains and to compare them to analyze DNA repair. We have used this approach to study interactions between DNA repair pathways in vivo. Additionally, we have implemented an ex vivo comet assay, in which nucleoids from treated and untreated cells were incubated ex vivo with cell-free protein extracts from individuals with distinct repair capacities. Four strains were used: wild-type OregonK (OK), nucleotide excision repair mutant mus201, dmPolQ protein mutant mus308, and the double mutant mus201;mus308. Methyl methanesulfonate (MMS) was used as a genotoxic agent. Both approaches were performed with neuroblasts from third-instar larvae; they detected the effects of the NER and dmPolQ pathways on the DDR to MMS and that they act additively in this response. Additionally, the ex vivo approach quantified that mus201, mus308, and the double mutant mus201;mus308 strains presented, respectively, 21.5%, 52.9%, and 14.8% of OK strain activity over MMS-induced damage. Considering the homology between mammals and Drosophila in repair pathways, the detected additive effect might be extrapolated even to humans, demonstrating that Drosophila might be an excellent model to study interactions between repair pathways.
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Affiliation(s)
- Rubén Rodríguez
- Department of Functional Biology (Genetic Area), University of Oviedo, 33006 Oviedo, Spain; (R.R.)
- Oncology University Institute from Asturias (IUOPA), University of Oviedo, 33006 Oviedo, Spain
| | - Isabel Gaivão
- Department of Genetics and Biotechnology and CECAV, University of Trás-os-Montes and Alto Douro, 5000-801 Vila Real, Portugal;
| | - Leticia Aguado
- Department of Functional Biology (Genetic Area), University of Oviedo, 33006 Oviedo, Spain; (R.R.)
- Oncology University Institute from Asturias (IUOPA), University of Oviedo, 33006 Oviedo, Spain
| | - Marta Espina
- Department of Functional Biology (Genetic Area), University of Oviedo, 33006 Oviedo, Spain; (R.R.)
- Oncology University Institute from Asturias (IUOPA), University of Oviedo, 33006 Oviedo, Spain
| | - Jorge García
- Department of Functional Biology (Genetic Area), University of Oviedo, 33006 Oviedo, Spain; (R.R.)
| | - Pablo Martínez-Camblor
- Department of Biomedical Data Science, Geisel Medical School at Dartmouth, Hanover, NH 03755, USA;
- Faculty of Health Sciences, Universidad Autónoma de Chile, Provedencia 7500912, Chile
| | - L. María Sierra
- Department of Functional Biology (Genetic Area), University of Oviedo, 33006 Oviedo, Spain; (R.R.)
- Oncology University Institute from Asturias (IUOPA), University of Oviedo, 33006 Oviedo, Spain
- Institute of Sanitary Research of the Principality of Asturias, Av. del Hospital Universitario, s/n, 33011 Oviedo, Spain
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14
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Møller P, Roursgaard M. Exposure to nanoplastic particles and DNA damage in mammalian cells. MUTATION RESEARCH. REVIEWS IN MUTATION RESEARCH 2023; 792:108468. [PMID: 37666295 DOI: 10.1016/j.mrrev.2023.108468] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/12/2023] [Revised: 08/30/2023] [Accepted: 08/30/2023] [Indexed: 09/06/2023]
Abstract
There is concern about human exposure to nanoplastics from intentional use or degradation of plastics in the environment. This review assesses genotoxic effects of nanoplastics, defined as particles with a primary size of less than 1000 nm. The majority of results on genotoxicity come from studies on polystyrene (PS) particles in mammalian cell cultures. Most studies have measured DNA strand breaks (standard comet assay), oxidatively damaged DNA (Fpg-modified comet assay) and micronuclei. Twenty-nine out of 60 results have shown statistically significant genotoxic effects by PS exposure in cell cultures. A statistical analysis indicates that especially modified PS particles are genotoxic (odds ratio = 8.6, 95 % CI: 1.6, 46) and immune cells seems to be more sensitive to genotoxicity than other cell types such as epithelial cells (odds ratio = 8.0, 95 % CI: 1.6, 39). On the contrary, there is not a clear association between statistically significant effects in genotoxicity tests and the primary size of PS particles, (i.e. smaller versus larger than 100 nm) or between the type of genotoxic endpoint (i.e. repairable versus permanent DNA lesions). Three studies of PS particle exposure in animals have shown increased level of DNA strand breaks in leukocytes and prefrontal cortex cells. Nanoplastics from polyethylene, propylene, polyvinyl chloride and polyethylene terephthalate have been investigated in very few studies and it is currently not possible to draw conclusion about their genotoxic hazard. In summary, there is some evidence suggesting that PS particles may be genotoxic in mammalian cells.
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Affiliation(s)
- Peter Møller
- Department of Public Health, Section of Environmental Health, University of Copenhagen, Øster Farimagsgade 5A, DK-1014 Copenhagen K, Denmark.
| | - Martin Roursgaard
- Department of Public Health, Section of Environmental Health, University of Copenhagen, Øster Farimagsgade 5A, DK-1014 Copenhagen K, Denmark
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15
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Mišík M, Staudinger M, Kundi M, Worel N, Nersesyan A, Ferk F, Dusinska M, Azqueta A, Møller P, Knasmueller S. Use of the Single Cell Gel Electrophoresis Assay for the Detection of DNA-protective Dietary Factors: Results of Human Intervention Studies. MUTATION RESEARCH. REVIEWS IN MUTATION RESEARCH 2023; 791:108458. [PMID: 37031732 DOI: 10.1016/j.mrrev.2023.108458] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/06/2022] [Revised: 03/14/2023] [Accepted: 04/06/2023] [Indexed: 04/11/2023]
Abstract
The single cell gel electrophoresis technique is based on the measurement of DNA migration in an electric field and enables to investigate via determination of DNA-damage the impact of foods and their constituents on the genetic stability. DNA-damage leads to adverse effects including cancer, neurodegenerative disorders and infertility. In the last 25 years approximately 90 human intervention trials have been published in which DNA-damage, formation of oxidized bases, alterations of the sensitivity towards reactive oxygen species and chemicals and of repair functions were investigated with this technique. In approximately 50% of the studies protective effects were observed. Pronounced protection was found with certain plant foods (spinach, kiwi fruits, onions), coffee, green tea, honey and olive oil. Also diets with increased contents of vegetables caused positive effects. Small amounts of certain phenolics (gallic acid, xanthohumol) prevented oxidative damage of DNA; with antioxidant vitamins and cholecalciferol protective effects were only detected after intake of doses that exceed the recommended daily uptake values. The evaluation of the quality of the studies showed that many have methodological shortcomings (lack of controls, no calibration of repair enzymes, inadequate control of the compliance and statistical analyses) which should be avoided in future investigations.
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Affiliation(s)
- Miroslav Mišík
- Center for Cancer Research, Medical University of Vienna, Borschkegasse 8a, A 1090 Vienna, Austria
| | - Marlen Staudinger
- Center for Cancer Research, Medical University of Vienna, Borschkegasse 8a, A 1090 Vienna, Austria
| | - Michael Kundi
- Center for Public Health, Department of Environmental Health, Medical University of Vienna, Vienna, Austria
| | - Nadine Worel
- Center for Cancer Research, Medical University of Vienna, Borschkegasse 8a, A 1090 Vienna, Austria
| | - Armen Nersesyan
- Center for Cancer Research, Medical University of Vienna, Borschkegasse 8a, A 1090 Vienna, Austria
| | - Franziska Ferk
- Center for Cancer Research, Medical University of Vienna, Borschkegasse 8a, A 1090 Vienna, Austria
| | - Maria Dusinska
- Health Effects Laboratory, Department of Environmental Chemistry, NILU-Norwegian Institute for Air Research, Instituttveien 18, 2002 Kjeller, Norway
| | - Amaya Azqueta
- Department of Pharmacology and Toxicology, University of Navarra, Pamplona, Spain
| | - Peter Møller
- Section of Environmental Health, Department of Public Health, University of Copenhagen, Denmark
| | - Siegfried Knasmueller
- Center for Cancer Research, Medical University of Vienna, Borschkegasse 8a, A 1090 Vienna, Austria.
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16
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Measuring DNA modifications with the comet assay: a compendium of protocols. Nat Protoc 2023; 18:929-989. [PMID: 36707722 DOI: 10.1038/s41596-022-00754-y] [Citation(s) in RCA: 105] [Impact Index Per Article: 105.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2021] [Accepted: 07/05/2022] [Indexed: 01/28/2023]
Abstract
The comet assay is a versatile method to detect nuclear DNA damage in individual eukaryotic cells, from yeast to human. The types of damage detected encompass DNA strand breaks and alkali-labile sites (e.g., apurinic/apyrimidinic sites), alkylated and oxidized nucleobases, DNA-DNA crosslinks, UV-induced cyclobutane pyrimidine dimers and some chemically induced DNA adducts. Depending on the specimen type, there are important modifications to the comet assay protocol to avoid the formation of additional DNA damage during the processing of samples and to ensure sufficient sensitivity to detect differences in damage levels between sample groups. Various applications of the comet assay have been validated by research groups in academia, industry and regulatory agencies, and its strengths are highlighted by the adoption of the comet assay as an in vivo test for genotoxicity in animal organs by the Organisation for Economic Co-operation and Development. The present document includes a series of consensus protocols that describe the application of the comet assay to a wide variety of cell types, species and types of DNA damage, thereby demonstrating its versatility.
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17
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Vodicka P, Vodenkova S, Horak J, Opattova A, Tomasova K, Vymetalkova V, Stetina R, Hemminki K, Vodickova L. An investigation of DNA damage and DNA repair in chemical carcinogenesis triggered by small-molecule xenobiotics and in cancer: Thirty years with the comet assay. MUTATION RESEARCH. GENETIC TOXICOLOGY AND ENVIRONMENTAL MUTAGENESIS 2023; 885:503564. [PMID: 36669813 DOI: 10.1016/j.mrgentox.2022.503564] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/29/2022] [Revised: 11/04/2022] [Accepted: 11/22/2022] [Indexed: 11/25/2022]
Abstract
In the present review we addressed the determination of DNA damage induced by small-molecule carcinogens, considered their persistence in DNA and mutagenicity in in vitro and in vivo systems over a period of 30 years. The review spans from the investigation of the role of DNA damage in the cascade of chemical carcinogenesis. In the nineties, this concept evolved into the biomonitoring studies comprising multiple biomarkers that not only reflected DNA/chromosomal damage, but also the potential of the organism for biotransformation/elimination of various xenobiotics. Since first years of the new millennium, dynamic system of DNA repair and host susceptibility factors started to appear in studies and a considerable knowledge has been accumulated on carcinogens and their role in carcinogenesis. It was understood that the final biological links bridging the arising DNA damage and cancer onset remain to be elucidated. In further years the community of scientists learnt that cancer is a multifactorial disease evolving over several decades of individual´s life. Moreover, DNA damage and DNA repair are inseparable players also in treatment of malignant diseases, but affect substantially other processes, such as degeneration. Functional monitoring of DNA repair pathways and DNA damage response may cast some light on above aspects. Very little is currently known about the relationship between telomere homeostasis and DNA damage formation and repair. DNA damage/repair in genomic and mitochondrial DNA and crosstalk between these two entities emerge as a new interesting topic.
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Affiliation(s)
- Pavel Vodicka
- Department of Molecular Biology of Cancer, Institute of Experimental Medicine of the Czech Academy of Sciences, 142 20 Prague, Czech Republic; Institute of Biology and Medical Genetics, First Faculty of Medicine, Charles University, 128 00 Prague, Czech Republic; Faculty of Medicine and Biomedical Centre in Pilsen, Charles University, 306 05 Pilsen, Czech Republic
| | - Sona Vodenkova
- Department of Molecular Biology of Cancer, Institute of Experimental Medicine of the Czech Academy of Sciences, 142 20 Prague, Czech Republic; Faculty of Medicine and Biomedical Centre in Pilsen, Charles University, 306 05 Pilsen, Czech Republic
| | - Josef Horak
- Department of Molecular Biology of Cancer, Institute of Experimental Medicine of the Czech Academy of Sciences, 142 20 Prague, Czech Republic
| | - Alena Opattova
- Department of Molecular Biology of Cancer, Institute of Experimental Medicine of the Czech Academy of Sciences, 142 20 Prague, Czech Republic; Institute of Biology and Medical Genetics, First Faculty of Medicine, Charles University, 128 00 Prague, Czech Republic; Faculty of Medicine and Biomedical Centre in Pilsen, Charles University, 306 05 Pilsen, Czech Republic
| | - Kristyna Tomasova
- Department of Molecular Biology of Cancer, Institute of Experimental Medicine of the Czech Academy of Sciences, 142 20 Prague, Czech Republic; Faculty of Medicine and Biomedical Centre in Pilsen, Charles University, 306 05 Pilsen, Czech Republic
| | - Veronika Vymetalkova
- Department of Molecular Biology of Cancer, Institute of Experimental Medicine of the Czech Academy of Sciences, 142 20 Prague, Czech Republic; Institute of Biology and Medical Genetics, First Faculty of Medicine, Charles University, 128 00 Prague, Czech Republic; Faculty of Medicine and Biomedical Centre in Pilsen, Charles University, 306 05 Pilsen, Czech Republic
| | - Rudolf Stetina
- Department of Research and Development, University Hospital Hradec Kralove, 500 03 Hradec Kralove, Czech Republic
| | - Kari Hemminki
- Faculty of Medicine and Biomedical Centre in Pilsen, Charles University, 306 05 Pilsen, Czech Republic; Division of Cancer Epidemiology, German Cancer Research Centre (DKFZ), 691 20 Heidelberg, Germany
| | - Ludmila Vodickova
- Department of Molecular Biology of Cancer, Institute of Experimental Medicine of the Czech Academy of Sciences, 142 20 Prague, Czech Republic; Institute of Biology and Medical Genetics, First Faculty of Medicine, Charles University, 128 00 Prague, Czech Republic; Faculty of Medicine and Biomedical Centre in Pilsen, Charles University, 306 05 Pilsen, Czech Republic.
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18
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Azqueta A, Stopper H, Zegura B, Dusinska M, Møller P. Do cytotoxicity and cell death cause false positive results in the in vitro comet assay? MUTATION RESEARCH. GENETIC TOXICOLOGY AND ENVIRONMENTAL MUTAGENESIS 2022; 881:503520. [PMID: 36031332 DOI: 10.1016/j.mrgentox.2022.503520] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/07/2021] [Revised: 06/10/2022] [Accepted: 06/21/2022] [Indexed: 10/17/2022]
Abstract
The comet assay is used to measure DNA damage induced by chemical and physical agents. High concentrations of test agents may cause cytotoxicity or cell death, which may give rise to false positive results in the comet assay. Systematic studies on genotoxins and cytotoxins (i.e. non-genotoxic poisons) have attempted to establish a threshold of cytotoxicity or cell death by which DNA damage results measured by the comet assay could be regarded as a false positive result. Thresholds of cytotoxicity/cell death range from 20% to 50% in various publications. Curiously, a survey of the latest literature on comet assay results from cell culture studies suggests that one-third of publications did not assess cytotoxicity or cell death. We recommend that it should be mandatory to include results from at least one type of assay on cytotoxicity, cell death or cell proliferation in publications on comet assay results. A combination of cytotoxicity (or cell death) and proliferation (or colony forming efficiency assay) is preferable in actively proliferating cells because it covers more mechanisms of action. Applying a general threshold of cytotoxicity/cell death to all types of agents may not be applicable; however, 25% compared to the concurrent negative control seems to be a good starting value to avoid false positive comet assay results. Further research is needed to establish a threshold value to distinguish between true and potentially false positive genotoxic effects detected by the comet assay.
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Affiliation(s)
- Amaya Azqueta
- Department of Pharmacology and Toxicology, University of Navarra, C/Irunlarrea 1, 31009 Pamplona, Spain and IdiSNA, Navarra Institute for Health Research, Pamplona, Spain.
| | - Helga Stopper
- Institute of Pharmacology and Toxicology, University of Würzburg, Versbacher Str. 9, 97078 Würzburg, Germany
| | - Bojana Zegura
- Department of Genetic Toxicology and Cancer Biology, National Institute of Biology, Večna pot 111, 1000 Ljubljana, Slovenia
| | - Maria Dusinska
- Health Effects Laboratory, Department of Environmental Chemistry, NILU-Norwegian Institute for Air Research, Instituttveien 18, 2002 Kjeller, Norway
| | - Peter Møller
- Department of Public Health, Section of Environmental Health, University of Copenhagen, Øster Farimagsgade 5A, DK-1014 Copenhagen, Denmark
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19
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Di Ianni E, Jacobsen NR, Vogel UB, Møller P. Systematic review on primary and secondary genotoxicity of carbon black nanoparticles in mammalian cells and animals. MUTATION RESEARCH. REVIEWS IN MUTATION RESEARCH 2022; 790:108441. [PMID: 36007825 DOI: 10.1016/j.mrrev.2022.108441] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/08/2022] [Revised: 08/17/2022] [Accepted: 08/19/2022] [Indexed: 01/01/2023]
Abstract
Carbon black exposure causes oxidative stress, inflammation and genotoxicity. The objective of this systematic review was to assess the contributions of primary (i.e. direct formation of DNA damage) and secondary genotoxicity (i.e., DNA lesions produced indirectly by inflammation) to the overall level of DNA damage by carbon black. The database is dominated by studies that have measured DNA damage by the comet assay. Cell culture studies indicate a genotoxic action of carbon black, which might be mediated by oxidative stress. Many in vivo studies originate from one laboratory that has investigated the genotoxic effects of Printex 90 in mice by intra-tracheal instillation. Meta-analysis and pooled analysis of these results demonstrate that Printex 90 exposure is associated with a slightly increased level of DNA strand breaks in bronchoalveolar lavage cells and lung tissue. Other types of genotoxic damage have not been investigated as thoroughly as DNA strand breaks, although there is evidence to suggest that carbon black exposure might increase the mutation frequency and cytogenetic endpoints. Stratification of studies according to concurrent inflammation and DNA damage does not indicate that carbon black exposure gives rise to secondary genotoxicity. Even substantial pulmonary inflammation is at best only associated with a weak genotoxic response in lung tissue. In conclusion, the review indicates that nanosized carbon black is a weak genotoxic agent and this effect is more likely to originate from a primary genotoxic mechanism of action, mediated by e.g., oxidative stress, than inflammation-driven (secondary) genotoxicity.
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Affiliation(s)
- Emilio Di Ianni
- The National Research Centre for the Working Environment, Lersø Parkalle 105, DK-2100 Copenhagen Ø, Denmark
| | - Nicklas Raun Jacobsen
- The National Research Centre for the Working Environment, Lersø Parkalle 105, DK-2100 Copenhagen Ø, Denmark
| | - Ulla Birgitte Vogel
- The National Research Centre for the Working Environment, Lersø Parkalle 105, DK-2100 Copenhagen Ø, Denmark; National Food Institute, Technical University of Denmark, Kemitorvet, Bygning 202, DK-2800 Kgs Lyngby, Denmark
| | - Peter Møller
- Department of Public Health, Section of Environmental Health, University of Copenhagen, Øster Farimagsgade 5A, DK-1014 Copenhagen, Denmark.
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20
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Hedyotis diffusae Herba-Andrographis Herba inhibits the cellular proliferation of nasopharyngeal carcinoma and triggers DNA damage through activation of p53 and p21. Cancer Gene Ther 2022; 29:973-983. [PMID: 34754077 DOI: 10.1038/s41417-021-00385-7] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2021] [Revised: 08/08/2021] [Accepted: 08/27/2021] [Indexed: 12/25/2022]
Abstract
Dysregulation of the cell cycle and the resulting aberrant cellular proliferation has been highlighted as a hallmark of cancer. Certain traditional Chinese medicines can inhibit cancer growth by inducing cell cycle arrest. In this study we explore the effect of Hedyotis diffusae Herba-Andrographis Herba on the cell cycle of nasopharyngeal carcinoma (NPC). Hedyotis diffusae Herba-Andrographis Herba-containing serum was prepared and then added to the cell culture medium. BrdU, comet, and FUCCI assays, western blot analysis and flow cytometry analysis revealed that Hedyotis diffusae Herba-Andrographis Herba treatment significantly alters cell proliferation, DNA damage, and cell cycle distribution. Xenograft mouse model experiments were performed, confirming these in vitro findings in vivo. Treatment with Hedyotis diffusae Herba-Andrographis Herba inhibited cell proliferation, promoted DNA damage, and arrested NPC cells progression from G1 to S phase. Further examination of the underlying molecular mechanisms revealed that treatment with Hedyotis diffusae Herba-Andrographis Herba increased the expression of p53 and p21, while reducing that of CCND1, Phospho-Rb, E2F1, γH2AX, and Ki-67 both in vivo and in vitro. Conversely, the inhibition of p53 and p21 could abolish the promoting effect of Hedyotis diffusae Herba-Andrographis Herba on the NPC cell cycle arrest at the G1 phase, contributing to the proliferation of NPC cells. Hedyotis diffusae Herba-Andrographis Herba suppressed the tumor growth in vivo. Overall, these findings suggest that Hedyotis Diffusae Herba-Andrographis prevent the progression of NPC by inducing NPC cell cycle arrest at the G1 phase through a p53/p21-dependent mechanism, providing a novel potential therapeutic treatment against NPC.
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21
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Xiong P, Huang X, Ye N, Lu Q, Zhang G, Peng S, Wang H, Liu Y. Cytotoxicity of Metal-Based Nanoparticles: From Mechanisms and Methods of Evaluation to Pathological Manifestations. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2022; 9:e2106049. [PMID: 35343105 PMCID: PMC9165481 DOI: 10.1002/advs.202106049] [Citation(s) in RCA: 33] [Impact Index Per Article: 16.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/28/2021] [Revised: 03/09/2022] [Indexed: 05/05/2023]
Abstract
Metal-based nanoparticles (NPs) are particularly important tools in tissue engineering-, drug carrier-, interventional therapy-, and biobased technologies. However, their complex and varied migration and transformation pathways, as well as their continuous accumulation in closed biological systems, cause various unpredictable toxic effects that threaten human and ecosystem health. Considerable experimental and theoretical efforts have been made toward understanding these cytotoxic effects, though more research on metal-based NPs integrated with clinical medicine is required. This review summarizes the mechanisms and evaluation methods of cytotoxicity and provides an in-depth analysis of the typical effects generated in the nervous, immune, reproductive, and genetic systems. In addition, the challenges and opportunities are discussed to enhance future investigations on safer metal-based NPs for practical commercial adoption.
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Affiliation(s)
- Peizheng Xiong
- TCM Regulating Metabolic Diseases Key Laboratory of Sichuan ProvinceHospital of Chengdu University of Traditional Chinese MedicineChengdu610072P. R. China
| | - Xiangming Huang
- The First Affiliated Hospital of Guangxi University of Traditional Chinese MedicineNanningGuangxi Province530023P. R. China
| | - Naijing Ye
- TCM Regulating Metabolic Diseases Key Laboratory of Sichuan ProvinceHospital of Chengdu University of Traditional Chinese MedicineChengdu610072P. R. China
| | - Qunwen Lu
- TCM Regulating Metabolic Diseases Key Laboratory of Sichuan ProvinceHospital of Chengdu University of Traditional Chinese MedicineChengdu610072P. R. China
| | - Gang Zhang
- TCM Regulating Metabolic Diseases Key Laboratory of Sichuan ProvinceHospital of Chengdu University of Traditional Chinese MedicineChengdu610072P. R. China
| | - Shunlin Peng
- TCM Regulating Metabolic Diseases Key Laboratory of Sichuan ProvinceHospital of Chengdu University of Traditional Chinese MedicineChengdu610072P. R. China
| | - Hongbo Wang
- Institute of Smart City and Intelligent TransportationSouthwest Jiaotong UniversityChengdu611700P. R. China
- State Key Laboratory of Electronic Thin Film and Integrated DevicesUniversity of Electronic Science and Technology of ChinaChengdu610054P. R. China
| | - Yiyao Liu
- TCM Regulating Metabolic Diseases Key Laboratory of Sichuan ProvinceHospital of Chengdu University of Traditional Chinese MedicineChengdu610072P. R. China
- Department of BiophysicsSchool of Life Science and TechnologyUniversity of Electronic Science and Technology of ChinaChengduSichuan610054P. R. China
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22
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Opattova A, Langie SAS, Milic M, Collins A, Brevik A, Coskun E, Dusinska M, Gaivão I, Kadioglu E, Laffon B, Marcos R, Pastor S, Slyskova J, Smolkova B, Szilágyi Z, Valdiglesias V, Vodicka P, Volkovova K, Bonassi S, Godschalk RWL. A pooled analysis of molecular epidemiological studies on modulation of DNA repair by host factors. MUTATION RESEARCH. GENETIC TOXICOLOGY AND ENVIRONMENTAL MUTAGENESIS 2022; 876-877:503447. [PMID: 35483778 DOI: 10.1016/j.mrgentox.2022.503447] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/28/2021] [Revised: 12/06/2021] [Accepted: 01/10/2022] [Indexed: 02/09/2023]
Abstract
Levels of DNA damage represent the dynamics between damage formation and removal. Therefore, to better interpret human biomonitoring studies with DNA damage endpoints, an individual's ability to recognize and properly remove DNA damage should be characterized. Relatively few studies have included DNA repair as a biomarker and therefore, assembling and analyzing a pooled database of studies with data on base excision repair (BER) was one of the goals of hCOMET (EU-COST CA15132). A group of approximately 1911 individuals, was gathered from 8 laboratories which run population studies with the comet-based in vitro DNA repair assay. BER incision activity data were normalized and subsequently correlated with various host factors. BER was found to be significantly higher in women. Although it is generally accepted that age is inversely related to DNA repair, no overall effect of age was found, but sex differences were most pronounced in the oldest quartile (>61 years). No effect of smoking or occupational exposures was found. A body mass index (BMI) above 25 kg/m2 was related to higher levels of BER. However, when BMI exceeded 35 kg/m2, repair incision activity was significantly lower. Finally, higher BER incision activity was related to lower levels of DNA damage detected by the comet assay in combination with formamidopyrimidine DNA glycosylase (Fpg), which is in line with the fact that oxidatively damaged DNA is repaired by BER. These data indicate that BER plays a role in modulating the steady-state level of DNA damage that is detected in molecular epidemiological studies and should therefore be considered as a parallel endpoint in future studies.
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Affiliation(s)
- Alena Opattova
- Department of the Molecular Biology of Cancer, Institute of Experimental Medicine of the Czech Academy of Sciences, Prague, 14200, Czech Republic; Institute of Biology and Medical Genetics, First Faculty of Medicine, Charles University, Prague, 12800, Czech Republic; Biomedical Centre, Faculty of Medicine in Pilsen, Charles University, Pilsen, 306 05, Czech Republic
| | - Sabine A S Langie
- Department of Pharmacology & Toxicology, School for Nutrition and Translational Research in Metabolism (NUTRIM), Maastricht University, the Netherlands
| | - Mirta Milic
- Mutagenesis Unit, Institute for Medical Research and Occupational Health, Zagreb, Croatia
| | | | - Asgeir Brevik
- Oslo Metropolitan University, Faculty of Health Sciences, PO Box 4, St. Olavs plass, 0130, Oslo, Norway
| | - Erdem Coskun
- Gazi University, Faculty of Pharmacy, Department of Toxicology, Etiler, Ankara, 06330, Turkey
| | - Maria Dusinska
- Health Effects Laboratory, Department of Environmental Chemistry, Norwegian Institute for Air Research (NILU), 2002, Kjeller, Norway
| | - Isabel Gaivão
- Genetics and Biotechnology Department and Veterinary and Animal Research Centre (CECAV), Universidade de Trás-os-Montes e Alto Douro, Vila Real, Portugal
| | - Ela Kadioglu
- Gazi University, Faculty of Pharmacy, Department of Toxicology, Etiler, Ankara, 06330, Turkey
| | - Blanca Laffon
- Instituto de Investigación Biomédica de A Coruña (INIBIC), AE CICA-INIBIC. Oza, 15071, A Coruña, Spain; Universidade da Coruña, Grupo DICOMOSA, Centro de Investigaciones Científicas Avanzadas (CICA), Departamento de Psicología, Facultad de Ciencias de la Educación, Campus Elviña s/n, 15071, A Coruña, Spain
| | - Ricard Marcos
- Group of Mutagenesis, Department of Genetics and Microbiology, Faculty of Biosciences, Universitat Autònoma de Barcelona, Cerdanyola del Vallès, Barcelona, Spain
| | - Susana Pastor
- Group of Mutagenesis, Department of Genetics and Microbiology, Faculty of Biosciences, Universitat Autònoma de Barcelona, Cerdanyola del Vallès, Barcelona, Spain
| | - Jana Slyskova
- Department of the Molecular Biology of Cancer, Institute of Experimental Medicine of the Czech Academy of Sciences, Prague, 14200, Czech Republic
| | - Bozena Smolkova
- Cancer Research Institute, Biomedical Research Center of the Slovak Academy of Sciences, 84505, Bratislava, Slovakia
| | - Zsófia Szilágyi
- Department of Non-ionizing Radiation, National Public Health Center, H-1221, Budapest, Hungary
| | - Vanessa Valdiglesias
- Instituto de Investigación Biomédica de A Coruña (INIBIC), AE CICA-INIBIC. Oza, 15071, A Coruña, Spain; Universidade da Coruña, Grupo DICOMOSA, Centro de Investigaciones Científicas Avanzadas (CICA), Departamento de Biología, Facultad de Ciencias, Campus A Zapateira s/n, 15071, A Coruña, Spain
| | - Pavel Vodicka
- Department of the Molecular Biology of Cancer, Institute of Experimental Medicine of the Czech Academy of Sciences, Prague, 14200, Czech Republic; Institute of Biology and Medical Genetics, First Faculty of Medicine, Charles University, Prague, 12800, Czech Republic; Biomedical Centre, Faculty of Medicine in Pilsen, Charles University, Pilsen, 306 05, Czech Republic
| | - Katarina Volkovova
- Department of Biology, Faculty of Medicine, Slovak Medical University, 833 03, Bratislava, Slovakia
| | - Stefano Bonassi
- Unit of Clinical and Molecular Epidemiology, IRCCS, San Raffaele Pisana, Rome, Italy; Department of Human Sciences and Quality of Life Promotion, San Raffaele University, Rome, Italy
| | - Roger W L Godschalk
- Department of Pharmacology & Toxicology, School for Nutrition and Translational Research in Metabolism (NUTRIM), Maastricht University, the Netherlands.
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Xue W, Zhang Q, Chang Y, Brennan JD, Li Y, Liu M. Quantifying DNA damage on paper sensors via controlled template-independent DNA polymerization. Chem Sci 2022; 13:6496-6501. [PMID: 35756503 PMCID: PMC9172109 DOI: 10.1039/d1sc04268h] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2021] [Accepted: 10/13/2021] [Indexed: 11/21/2022] Open
Abstract
Terminal deoxynucleotidyl transferase (TdT) catalyzes template-independent DNA synthesis in a well-controllable mode on paper, allowing absolute quantification of polymetric labeling of a single 3′-OH present on genomic DNA.
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Affiliation(s)
- Wei Xue
- School of Environmental Science and Technology, Key Laboratory of Industrial Ecology and Environmental Engineering, Ministry of Education, Dalian University of Technology, Dalian, 116024, China
| | - Qiang Zhang
- School of Bioengineering, Dalian University of Technology, Dalian 116024, China
| | - Yangyang Chang
- School of Environmental Science and Technology, Key Laboratory of Industrial Ecology and Environmental Engineering, Ministry of Education, Dalian University of Technology, Dalian, 116024, China
- Dalian POCT Laboratory, Dalian 116024, China
| | - John D. Brennan
- Biointerfaces Institute, McMaster University, 1280 Main Street West, Hamilton, Ontario, L8S4O3, Canada
| | - Yingfu Li
- Department of Biochemistry and Biomedical Sciences, McMaster University, 1280 Main Street West, Hamilton, Ontario, L8S4K1, Canada
| | - Meng Liu
- School of Environmental Science and Technology, Key Laboratory of Industrial Ecology and Environmental Engineering, Ministry of Education, Dalian University of Technology, Dalian, 116024, China
- Dalian POCT Laboratory, Dalian 116024, China
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24
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Measurement of oxidatively damaged DNA in mammalian cells using the comet assay: Reflections on validity, reliability and variability. MUTATION RESEARCH. GENETIC TOXICOLOGY AND ENVIRONMENTAL MUTAGENESIS 2022; 873:503423. [PMID: 35094807 DOI: 10.1016/j.mrgentox.2021.503423] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/31/2021] [Revised: 10/27/2021] [Accepted: 11/03/2021] [Indexed: 11/24/2022]
Abstract
The comet assay is a simple technique for measurements of low levels of DNA damage and repair in single cells. However, there is variation in background levels of DNA damage in peripheral blood mononuclear cells (PBMCs). This variation has been documented by inter-laboratory ring-trials where identical samples have been analysed in different laboratories using the formamidopyrimidine DNA glycosylase (Fpg)-modified comet assay. The coefficient of variation of background levels of Fpg-sensitive sites was 128 % in the first inter-laboratory validation trial called European Standards Committee on Oxidative DNA Damage. The variation was reduced to 44 % by the end of the project. Subsequent ring-trials by the European Comet Assay Validation Group showed similar inter-laboratory variation in Fpg-sensitive sites in PBMCs (45 %). The lowest inter-laboratory variation in Fpg-sensitive sites in PBMCs was 12 % when using calibration to standardize comet assay descriptors. Introduction of standard comet assay procedures was surprisingly unsuccessful as certain laboratories experienced technical problems using unaccustomed assay conditions. This problem was alleviated by using flexible assay standard conditions rather than a standard protocol in a ring-trial by the hCOMET group. The approach reduced technical problems, but the inter-laboratory variation in Fpg-sensitive sites was not reduced. The ring-trials have not pinpointed specific assay steps as major determinants of the variation in DNA damage levels. It is likely that small differences in several steps cause inter-laboratory variation. Although this variation in reported DNA damage levels causes concern, ring-trials have also shown that the comet assay is a reliable tool in biomonitoring studies.
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25
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Bankoglu EE, Schuele C, Stopper H. Cell survival after DNA damage in the comet assay. Arch Toxicol 2021; 95:3803-3813. [PMID: 34609522 PMCID: PMC8536587 DOI: 10.1007/s00204-021-03164-3] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2021] [Accepted: 09/16/2021] [Indexed: 11/26/2022]
Abstract
The comet assay is widely used in basic research, genotoxicity testing, and human biomonitoring. However, interpretation of the comet assay data might benefit from a better understanding of the future fate of a cell with DNA damage. DNA damage is in principle repairable, or if extensive, can lead to cell death. Here, we have correlated the maximally induced DNA damage with three test substances in TK6 cells with the survival of the cells. For this, we selected hydrogen peroxide (H2O2) as an oxidizing agent, methyl methanesulfonate (MMS) as an alkylating agent and etoposide as a topoisomerase II inhibitor. We measured cell viability, cell proliferation, apoptosis, and micronucleus frequency on the following day, in the same cell culture, which had been analyzed in the comet assay. After treatment, a concentration dependent increase in DNA damage and in the percentage of non-vital and apoptotic cells was found for each substance. Values greater than 20-30% DNA in tail caused the death of more than 50% of the cells, with etoposide causing slightly more cell death than H2O2 or MMS. Despite that, cells seemed to repair of at least some DNA damage within few hours after substance removal. Overall, the reduction of DNA damage over time is due to both DNA repair and death of heavily damaged cells. We recommend that in experiments with induction of DNA damage of more than 20% DNA in tail, survival data for the cells are provided.
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Affiliation(s)
- Ezgi Eyluel Bankoglu
- Institute of Pharmacology and Toxicology, University of Wuerzburg, Versbacher Straße 9, 97078, Wuerzburg, Germany
| | - Carolin Schuele
- Institute of Pharmacology and Toxicology, University of Wuerzburg, Versbacher Straße 9, 97078, Wuerzburg, Germany
| | - Helga Stopper
- Institute of Pharmacology and Toxicology, University of Wuerzburg, Versbacher Straße 9, 97078, Wuerzburg, Germany.
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26
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Higgs EB, Godschalk R, Langie SAS, van Schooten FJ, Hodges NJ. Upregulation of mNEIL3 in Ogg1-null cells is a potential backup mechanism for 8-oxoG repair. Mutagenesis 2021; 36:437-444. [PMID: 34644377 DOI: 10.1093/mutage/geab038] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2021] [Accepted: 10/12/2021] [Indexed: 11/13/2022] Open
Abstract
Reactive oxygen species formation and resultant oxidative damage to DNA are ubiquitous events in cells, the homeostasis of which can be dysregulated in a range of pathological conditions. Base excision repair (BER) is the primary repair mechanism for oxidative genomic DNA damage. One prevalent oxidised base modification, 8-oxoguanine (8-oxoG), is recognised by 8-oxoguanine glycosylase-1 (OGG1) initiating removal and repair via BER. Surprisingly, Ogg1 null mouse embryonic fibroblasts (mOgg1-/- MEFs) do not accumulate 8-oxoG in the genome to the extent expected. This suggests that there are backup repair mechanisms capable of repairing 8-oxoG in the absence of OGG1. In the current study, we identified components of NER (Ercc1, Ercc4, Ercc5), BER (Lig1, Tdg, Nthl1, Mpg, Mgmt, NEIL3), MMR (Mlh1, Msh2, Msh6) and DSB (Brip1, Rad51d, Prkdc) pathways that are transcriptionally elevated in mOgg1-/- MEFs. Interestingly, all three nucleotide excision repair genes identified: Ercc1 (2.5 ± 0.2-fold), Ercc4 (1.5 ± 0.1-fold) and Ercc5 (1.7 ± 0.2-fold) have incision activity. There was also a significant functional increase in NER activity (42.0 ± 7.9%) compared to WT MEFs. We also observed upregulation of both Neil3 mRNA (37.9 ± 1.6-fold) and protein in mOgg1-/- MEFs. This was associated with a 3.4 ± 0.4-fold increase in NEIL3 substrate sites in genomic DNA of cells treated with BSO, consistent with the ability of NEIL3 to remove 8-oxoG oxidation products from genomic DNA. In conclusion, we suggest that in Ogg1-null cells, upregulation of multiple DNA repair proteins including incision components of the NER pathway and Neil3 are important compensatory responses to prevent the accumulation of genomic 8-oxoG.
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Affiliation(s)
- Ellen B Higgs
- School of Biosciences, The University of Birmingham, Birmingham, UK.,Department of Pharmacology & Toxicology, School for Nutrition and Translational Research in Metabolism, Maastricht University, Maastricht, Netherlands
| | - Roger Godschalk
- Department of Pharmacology & Toxicology, School for Nutrition and Translational Research in Metabolism, Maastricht University, Maastricht, Netherlands
| | - Sabine A S Langie
- Department of Pharmacology & Toxicology, School for Nutrition and Translational Research in Metabolism, Maastricht University, Maastricht, Netherlands
| | - Frederik-Jan van Schooten
- Department of Pharmacology & Toxicology, School for Nutrition and Translational Research in Metabolism, Maastricht University, Maastricht, Netherlands
| | - Nikolas J Hodges
- School of Biosciences, The University of Birmingham, Birmingham, UK
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27
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Xue W, Dan Zhao, Zhang Q, Chang Y, Liu M. An origami paper-based analytical device for DNA damage analysis. Chem Commun (Camb) 2021; 57:11465-11468. [PMID: 34651618 DOI: 10.1039/d1cc05019b] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Detection and characterization of DNA damage plays a critical role in genotoxicity testing, drug screening, and environmental health. We developed a fully integrated origami paper-based analytical device (oPAD) for measuring DNA damage. This simple device allows on-paper cell lysis, DNA extraction, terminal deoxynucleotidyl transferase dUTP nick end labeling (TUNEL) reaction and signal readout with simple operation steps, enabling rapid (within 30 min) and high throughput assessment of multiple DNA damages induced by exogenous chemical agents.
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Affiliation(s)
- Wei Xue
- School of Environmental Science and Technology, Key Laboratory of Industrial Ecology and Environmental Engineering (Ministry of Education), Dalian University of Technology, Dalian, 116024 (China); Dalian POCT laboratory, Dalian, 116024, China.
| | - Dan Zhao
- School of Environmental Science and Technology, Key Laboratory of Industrial Ecology and Environmental Engineering (Ministry of Education), Dalian University of Technology, Dalian, 116024 (China); Dalian POCT laboratory, Dalian, 116024, China.
| | - Qiang Zhang
- School of Bioengineering, Dalian University of Technology, Dalian 116024, China
| | - Yangyang Chang
- School of Environmental Science and Technology, Key Laboratory of Industrial Ecology and Environmental Engineering (Ministry of Education), Dalian University of Technology, Dalian, 116024 (China); Dalian POCT laboratory, Dalian, 116024, China.
| | - Meng Liu
- School of Environmental Science and Technology, Key Laboratory of Industrial Ecology and Environmental Engineering (Ministry of Education), Dalian University of Technology, Dalian, 116024 (China); Dalian POCT laboratory, Dalian, 116024, China.
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28
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Ocolotobiche EE, Dauder RM, Güerci AM. Radiosensitivity of radiotherapy patients: The effect of individual DNA repair capacity. MUTATION RESEARCH-GENETIC TOXICOLOGY AND ENVIRONMENTAL MUTAGENESIS 2021; 867:503371. [PMID: 34266627 DOI: 10.1016/j.mrgentox.2021.503371] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/23/2021] [Revised: 06/01/2021] [Accepted: 06/02/2021] [Indexed: 11/27/2022]
Abstract
Individual radiosensitivity is a critical problem in radiotherapy because of the treatment restrictions it imposes. We have tested whether induction/repair of genomic lesions correlates with the acute cutaneous effects of radiotherapy. Peripheral blood samples of 56 healthy volunteers and 18 patients with breast cancer were studied. DNA damage and DNA repair capacity were assessed in vitro (alkaline comet assay). Patients without skin reaction did not show significant differences from healthy individuals, with respect to either initial or radiation-induced DNA damage. Similar DNA repair kinetics, fitting a decreasing exponential response, were observed in both groups, and there were no significant differences in residual genotoxic damage. In contrast, patients exhibiting acute side effects showed significantly lower DNA repair ability and significantly more residual damage, compared to patients without radiotoxicity. This approach may help to identify patients who are at greater risk of radiotherapy side effects. However, many other factors, such as dosimetry, irradiated volume, and lifestyle should also be considered in the evaluation of individual radiosensitivity.
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Affiliation(s)
- Eliana E Ocolotobiche
- IGEVET - Instituto de Genética Veterinaria "Ing. Fernando N. Dulout" (UNLP-CONICET LA PLATA), Facultad de Ciencias Veterinarias, Universidad Nacional de La Plata, Calle 60 y 118 s/n (CP 1900) La Plata, Buenos Aires, Argentina; Facultad de Ciencias Exactas, Universidad Nacional de La Plata, Calle 47 y 115 s/n (CP 1900) La Plata, Buenos Aires, Argentina; Terapia Radiante S.A. Red CIO - La Plata, Calle 60 Nº 480 (CP 1900) La Plata, Buenos Aires, Argentina
| | - Ricard Marcos Dauder
- Grup de Mutagènesi, Departament de Genètica i de Microbiologia, Facultat de Biociències, Universitat Autónoma de Barcelona Campus de Bellaterra, 08193 Cerdanyola del Vallés, Spain
| | - Alba Mabel Güerci
- IGEVET - Instituto de Genética Veterinaria "Ing. Fernando N. Dulout" (UNLP-CONICET LA PLATA), Facultad de Ciencias Veterinarias, Universidad Nacional de La Plata, Calle 60 y 118 s/n (CP 1900) La Plata, Buenos Aires, Argentina; Facultad de Ciencias Exactas, Universidad Nacional de La Plata, Calle 47 y 115 s/n (CP 1900) La Plata, Buenos Aires, Argentina; Terapia Radiante S.A. Red CIO - La Plata, Calle 60 Nº 480 (CP 1900) La Plata, Buenos Aires, Argentina.
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29
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Møller P, Wils RS, Di Ianni E, Gutierrez CAT, Roursgaard M, Jacobsen NR. Genotoxicity of multi-walled carbon nanotube reference materials in mammalian cells and animals. MUTATION RESEARCH. REVIEWS IN MUTATION RESEARCH 2021; 788:108393. [PMID: 34893158 DOI: 10.1016/j.mrrev.2021.108393] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/17/2021] [Revised: 08/19/2021] [Accepted: 08/19/2021] [Indexed: 02/07/2023]
Abstract
Carbon nanotubes (CNTs) were the first nanomaterials to be evaluated by the International Agency for Research on Cancer (IARC). The categorization as possibly carcinogenic agent to humans was only applicable to multi-walled carbon nanotubes called MWCNT-7. Other types of CNTs were not classifiable because of missing data and it was not possible to pinpoint unique CNT characteristics that cause cancer. Importantly, the European Commission's Joint Research Centre (JRC) has established a repository of industrially manufactured nanomaterials that encompasses at least four well-characterized MWCNTs called NM-400 to NM-403 (original JRC code). This review summarizes the genotoxic effects of these JRC materials and MWCNT-7. The review consists of 36 publications with results on cell culture experiments (22 publications), animal models (9 publications) or both (5 publications). As compared to the publications in the IARC monograph on CNTs, the current database represents a significant increase as there is only an overlap of 8 publications. However, the results come mainly from cell cultures and/or measurements of DNA strand breaks by the comet assay and the micronucleus assay (82 out of 97 outcomes). A meta-analysis of cell culture studies on DNA strand breaks showed a genotoxic response by MWCNT-7, less consistent effect by NM-400 and NM-402, and least consistent effect by NM-401 and NM-403. Results from other in vitro tests indicate strongest evidence of genotoxicity for MWCNT-7. There are too few observations from animal models and humans to make general conclusions about genotoxicity.
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Affiliation(s)
- Peter Møller
- Department of Public Health, Section of Environmental Health, University of Copenhagen, Øster Farimagsgade 5A, DK-1014, Copenhagen K, Denmark.
| | - Regitze Sølling Wils
- Department of Public Health, Section of Environmental Health, University of Copenhagen, Øster Farimagsgade 5A, DK-1014, Copenhagen K, Denmark; The National Research Centre for the Working Environment, Lersø Parkalle 105, DK-2100, Copenhagen Ø, Denmark
| | - Emilio Di Ianni
- The National Research Centre for the Working Environment, Lersø Parkalle 105, DK-2100, Copenhagen Ø, Denmark
| | - Claudia Andrea Torero Gutierrez
- Department of Public Health, Section of Environmental Health, University of Copenhagen, Øster Farimagsgade 5A, DK-1014, Copenhagen K, Denmark; The National Research Centre for the Working Environment, Lersø Parkalle 105, DK-2100, Copenhagen Ø, Denmark
| | - Martin Roursgaard
- Department of Public Health, Section of Environmental Health, University of Copenhagen, Øster Farimagsgade 5A, DK-1014, Copenhagen K, Denmark
| | - Nicklas Raun Jacobsen
- The National Research Centre for the Working Environment, Lersø Parkalle 105, DK-2100, Copenhagen Ø, Denmark
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30
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Gajski G, Ravlić S, Godschalk R, Collins A, Dusinska M, Brunborg G. Application of the comet assay for the evaluation of DNA damage in mature sperm. MUTATION RESEARCH. REVIEWS IN MUTATION RESEARCH 2021; 788:108398. [PMID: 34893163 DOI: 10.1016/j.mrrev.2021.108398] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/07/2021] [Revised: 10/26/2021] [Accepted: 11/05/2021] [Indexed: 06/14/2023]
Abstract
DNA integrity is considered an important parameter of semen quality and is of significant value as a predictor of male fertility. Currently, there are several methods that can assess sperm DNA integrity. One such assay is the comet assay, or single-cell gel electrophoresis, which is a simple, sensitive, reliable, quick and low-cost technique that is used for measuring DNA strand breaks and repair at the level of individual cells. Although the comet assay is usually performed with somatic cells from different organs, the assay has the ability to detect genotoxicity in germ cells at different stages of spermatogenesis. Since the ability of sperm to remove DNA damage differs between the stages, interpretation of the results is dependent on the cells used. In this paper we give an overview on the use and applications of the comet assay on mature sperm and its ability to detect sperm DNA damage in both animals and humans. Overall, it can be concluded that the presence in sperm of significantly damaged DNA, assessed by the comet assay, is related to male infertility and seems to reduce live births. Although there is some evidence that sperm DNA damage also has a long-term impact on offspring's health, this aspect of DNA damage in sperm is understudied and deserves further attention. In summary, the comet assay can be applied as a useful tool to study effects of genotoxic exposures on sperm DNA integrity in animals and humans.
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Affiliation(s)
- Goran Gajski
- Institute for Medical Research and Occupational Health, Mutagenesis Unit, Zagreb, Croatia.
| | - Sanda Ravlić
- University of Zagreb, Centre for Research and Knowledge Transfer in Biotechnology, Zagreb, Croatia
| | - Roger Godschalk
- Maastricht University, School for Nutrition and Translational Research in Metabolism (NUTRIM), Department of Pharmacology & Toxicology, Maastricht, the Netherlands
| | - Andrew Collins
- University of Oslo, Institute of Basic Medical Sciences, Department of Nutrition, Oslo, Norway
| | - Maria Dusinska
- Norwegian Institute for Air Research (NILU), Department of Environmental Chemistry, Health Effects Laboratory, Kjeller, Norway
| | - Gunnar Brunborg
- Norwegian Institute of Public Health (NIPH), Section of Molecular Toxicology, Department of Environmental Health, Oslo, Norway
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31
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Møller P, Bankoglu EE, Stopper H, Giovannelli L, Ladeira C, Koppen G, Gajski G, Collins A, Valdiglesias V, Laffon B, Boutet-Robinet E, Perdry H, Del Bo' C, Langie SAS, Dusinska M, Azqueta A. Collection and storage of human white blood cells for analysis of DNA damage and repair activity using the comet assay in molecular epidemiology studies. Mutagenesis 2021; 36:193-212. [PMID: 33755160 DOI: 10.1093/mutage/geab012] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2020] [Accepted: 03/22/2021] [Indexed: 01/08/2023] Open
Abstract
DNA damage and repair activity are often assessed in blood samples from humans in different types of molecular epidemiology studies. However, it is not always feasible to analyse the samples on the day of collection without any type of storage. For instance, certain studies use repeated sampling of cells from the same subject or samples from different subjects collected at different time-points, and it is desirable to analyse all these samples in the same comet assay experiment. In addition, flawless comet assay analyses on frozen samples open up the possibility of using this technique on biobank material. In this article we discuss the use of cryopreserved peripheral blood mononuclear cells (PBMCs), buffy coat (BC) and whole blood (WB) for analysis of DNA damage and repair using the comet assay. The published literature and the authors' experiences indicate that various types of blood samples can be cryopreserved with only a minor effect on the basal level of DNA damage. There is evidence to suggest that WB and PBMCs can be cryopreserved for several years without much effect on the level of DNA damage. However, care should be taken when cryopreserving WB and BCs. It is possible to use either fresh or frozen samples of blood cells, but results from fresh and frozen cells should not be used in the same dataset. The article outlines detailed protocols for the cryopreservation of PBMCs, BCs and WB samples.
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Affiliation(s)
- Peter Møller
- Section of Environmental Health, Department of Public Health, University of Copenhagen, Øster Farimagsgade 5A, DK-1014 Copenhagen K, Denmark
| | - Ezgi Eyluel Bankoglu
- Institute of Pharmacology and Toxicology, University of Wuerzburg, Versbacher Str. 9, 97078 Wuerzburg, Germany
| | - Helga Stopper
- Institute of Pharmacology and Toxicology, University of Wuerzburg, Versbacher Str. 9, 97078 Wuerzburg, Germany
| | - Lisa Giovannelli
- Department NEUROFARBA, University of Florence, Viale G. Pieraccini 6, 50139 Florence, Italy
| | - Carina Ladeira
- H&TRC - Health & Technology Research Center, Escola Superior de Tecnologia da Saúde (ESTeSL), Instituto Politécnico de Lisboa, Avenida D. João II, lote 4.69.01, Parque das Nações, 1990-096 Lisboa, Portugal.,NOVA National School of Public Health, Public Health Research Centre, Universidade NOVA de Lisboa, Lisbon, Portugal.,Comprehensive Health Research Center (CHRC), Universidade NOVA de Lisboa, Portugal
| | | | - Goran Gajski
- Mutagenesis Unit, Institute for Medical Research and Occupational Health, Ksaverska cesta 2, 10000 Zagreb, Croatia
| | - Andrew Collins
- Department of Nutrition, Institute of Basic Medical Sciences, University of Oslo, Sognsvannsveien 9, 0372 Oslo, Norway
| | - Vanessa Valdiglesias
- Grupo DICOMOSA, Centro de Investigaciones Científicas Avanzadas (CICA), Departamento de Biología, Facultad de Ciencias, Universidade da Coruña, Campus A Zapateira s/n, 15071, A Coruña, Spain.,Instituto de Investigación Biomédica de A Coruña (INIBIC), AE CICA-INIBIC, Oza, 15071 A Coruña, Spain
| | - Blanca Laffon
- Instituto de Investigación Biomédica de A Coruña (INIBIC), AE CICA-INIBIC, Oza, 15071 A Coruña, Spain.,Grupo DICOMOSA, Centro de Investigaciones Científicas Avanzadas (CICA), Departamento de Psicología, Facultad de Ciencias de la Educación, Universidade da Coruña, Campus Elviña s/n, 15071, A Coruña, Spain
| | - Elisa Boutet-Robinet
- Toxalim (Research Centre in Food Toxicology), Université de Toulouse, INRAE, ENVT, INP-Purpan, UPS, Toulouse, France
| | - Hervé Perdry
- Université Paris-Saclay, UVSQ, Inserm, CESP, 94807, Villejuif, France
| | - Cristian Del Bo'
- Department of Food, Environmental and Nutritional Sciences (DeFENS), University of Milan, Via Celoria 2, 20133, Milan, Italy
| | - Sabine A S Langie
- School of Nutrition and Translational Research in Metabolism, Department of Pharmacology and Toxicology, University of Maastricht, Universiteitssingel 50, 6200 MD, Maastricht, The Netherlands
| | - Maria Dusinska
- Environmental Chemistry Department, Health Effects Laboratory, NILU - Norwegian Institute for Air Research, 2027 Kjeller, Norway
| | - Amaya Azqueta
- Department of Pharmacology and Toxicology, University of Navarra, C/Irunlarrea 1, 31008 Pamplona, Spain.,IdiSNA, Navarra Institute for Health Research, C/Irunlarrea 3, 31008 Pamplona, Spain
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